Quick viewing(Text Mode)

A Taxonomic Note on the Genus Lactobacillus

A Taxonomic Note on the Genus Lactobacillus

Taxonomic Description template

1 A taxonomic note on the : 2 Description of 23 novel genera, emended description 3 of the genus Lactobacillus Beijerinck 1901, and union 4 of and Leuconostocaceae 5 Jinshui Zheng1, $, Stijn Wittouck2, $, Elisa Salvetti3, $, Charles M.A.P. Franz4, Hugh M.B. Harris5, Paola 6 Mattarelli6, Paul W. O’Toole5, Bruno Pot7, Peter Vandamme8, Jens Walter9, 10, Koichi Watanabe11, 12, 7 Sander Wuyts2, Giovanna E. Felis3, #*, Michael G. Gänzle9, 13#*, Sarah Lebeer2 # 8 '© [Jinshui Zheng, Stijn Wittouck, Elisa Salvetti, Charles M.A.P. Franz, Hugh M.B. Harris, Paola 9 Mattarelli, Paul W. O’Toole, Bruno Pot, Peter Vandamme, Jens Walter, Koichi Watanabe, Sander 10 Wuyts, Giovanna E. Felis, Michael G. Gänzle, Sarah Lebeer]. 11 The definitive peer reviewed, edited version of this article is published in International Journal of 12 Systematic and Evolutionary Microbiology, https://doi.org/10.1099/ijsem.0.004107 13 1Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Hubei Key 14 Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, P.R. China. 15 2Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience 16 Engineering, University of Antwerp, Antwerp, Belgium 17 3 Dept. of Biotechnology, University of Verona, Verona, Italy 18 4 Max Rubner‐Institut, Department of Microbiology and Biotechnology, Kiel, Germany 19 5 School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland 20 6 University of Bologna, Dept. of Agricultural and Food Sciences, Bologna, Italy 21 7 Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit 22 Brussel, Brussels, Belgium 23 8 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, 24 Belgium 25 9 Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada 26 10 Department of Biological Sciences, University of Alberta, Edmonton, Canada 27 11 National Taiwan University, Dept. of Animal Science and Technology, Taipei, Taiwan R.O.C.; 28 12 Food Industry Research and Development Institute, Bioresource Collection and Research Center, 29 Hsinchu, Taiwan R.O.C. 30 13 Hubei University of Technology, College of Bioengineering and Food Science, Wuhan, Hubei, P.R. 31 China. 32 33 $ indicates shared first authorship; 34 # indicates shared last authorship 35 *corresponding authors; 36 Giovanna E. Felis, University of Verona, Dept. of Biotechnology, Strada le Grazie 15, 37134 Verona, tel: 37 +39 045 6835627; email: [email protected]; 38 Michael G. Gänzle, University of Alberta, Dept. of AFNS, 4‐10 Ag/For Centre, Edmonton, AB, Canada, 39 T6G 2P5, tel: + 1 780 492 0774; mail: [email protected] 40 41

42 ABSTRACT 43 The genus Lactobacillus comprises 262 (March 2020) that are extremely diverse at phenotypic, 44 ecological, and genotypic levels. This study evaluated the of Lactobacillaceae and 45 Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included 46 core genome phylogeny, (conserved) pairwise average amino identity, clade‐specific signature 47 genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we 48 propose reclassification of the genus Lactobacillus into 25 genera including the emended genus 49 Lactobacillus, which includes host‐adapted organisms that have been referred to as the L. delbrueckii 50 group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, 51 Bombilactobacillus, , Lapidilactobacillus, Agrilactobacillus, 52 Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, 53 Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, 54 Limosilactobacillus, , Acetilactobacillus, Apilactobacillus, Levilactobacillus, 55 Secundilactobacillus, and Lentilactobacillus are proposed. We also propose to emend the description 56 of the family Lactobacillaceae to include all genera that were previously included in families 57 Lactobacillaceae and Leuconostocaceae. The generic germ “lactobacilli” will remain useful to 58 designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects 59 the phylogenetic position of the micro‐organisms, and groups lactobacilli into robust clades with 60 shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus 61 encompassing species adapted to vertebrates (such as L. delbrueckii, L. iners, L. crispatus, L. jensensii 62 L. johnsonii, and L. acidophilus) or invertebrates (such as L. apis and L. bombicola).

63 64

2

65 INTRODUCTION 66 The genus Lactobacillus was proposed by Beijerinck in 1901 and includes Gram‐positive, fermentative, 67 facultatively anaerobic and non‐sporeforming . The genus is classified in the 68 , class , order Lactobacillales, family Lactobacillaceae, which contains the genera 69 Lactobacillus, Paralactobacillus and . The Leuconostocaceae, including the genera 70 Convivina, Fructobacillus, , and , are the closest relative at the family 71 level [1]. 72 The early taxonomy of lactobacilli was based on phenotypic traits including optimal growth 73 temperature, sugar utilization, and spectrum of metabolites produced [2]. Later in the 20th century, 74 genotypic and chemotaxonomic criteria including DNA‐DNA hybridisation, the mol% GC content and 75 the chemical structure of the were used for delineation of new bacterial species. Since 76 1983, the similarity of 16S rRNA genes has been used in bacterial taxonomy to provide phylogenetic 77 schemes as backbones for classification and nomenclature [3]. Within the last 15 years, the 78 sequencing of whole bacterial genomes became widely available and average nucleotide identity (ANI) 79 values of genes shared between two bacterial genomes was introduced as the gold standard for 80 delineation of new bacterial species [4, 5]. Although proposals have been made to apply a method‐ 81 free species concept that is based on cohesive evolutionary forces [6], an ANI value of 95% (94 – 96%) 82 has been almost consistently used in recent years to describe new bacterial species [7, 8] and was 83 suggested to reflect biological significance of the prokaryotic species concept [9]. Published species of 84 Lactobacillaceae and Leuconostocaceae were recently evaluated based on single‐copy core genes and 85 a fixed genome‐genome similarity cutoff; the species were exclusive and discontinuous [10]. 86 The introduction of genotypic methods such as 16S rRNA‐based phylogeny already revealed the 87 extensive diversity of the genus Lactobacillus, which includes the genus Pediococcus as an integral part 88 [11–13]. Phylogenetic trees on the basis of single genes including the 16S rRNA gene allow grouping 89 of species to phylogenetic clades, however, they do not have sufficient resolution to inform on the 90 phylogenetic relationships of different clades [13, 14]. Phylogenetic studies of lactobacilli and 91 pediococci on the basis of core genome phylogeny confirmed this phylogenetic heterogeneity; in 92 addition the greater resolution of core genome phylogeny established the presence of consistent 93 clades or phylogroups that are characterized by common phenotypic and ecological traits [12–17]. 94 Physiological and phylogenetic considerations, and genomic analyses also replaced the earlier 95 differentiation between “obligate homofermentative”, “facultative heterofermentative” and 96 “obligate heterofermentative” with a simpler differentiation of homofermentative 97 that metabolize hexoses via the Embden‐Meyerhoff pathway to pyruvate as the 98 key metabolic intermediate, and heterofermentative lactic acid bacteria, that metabolize hexoses via 99 the phosphoketolase pathway to pyruvate and acetyl‐phosphate as key intermediates [14, 18]. Within 100 the genus Lactobacillus, homofermentative and heterofermentative lactobacilli form distinct 101 phylogenetic clades [14, 16], while homolactic or heterolactic is conserved in other lactic 102 acid bacteria at the family level. Pentose metabolism, however, is variable at the species or strain level 103 [14]. 104 It has been increasingly recognized that the genus Lactobacillus as currently defined displays a level 105 of genetic diversity that by far exceeds what is generally found in bacterial genera and even bacterial 106 families. The different phylogroups within the genus, however, are composed of species with a 107 phylogenetic and physiological diversity that match the diversity of other bacterial genera [14]. Since 108 2015, several large‐scale phylogenetic analyses based on core genome phylogeny of a comprehensive 109 representation of species of the genera Lactobacillus and Pediococcus have revealed the discrepancy 110 between the taxonomy of these genera and other bacterial genera [14, 16, 17]. The continuous species

3

111 descriptions in the last years ‐ 81 since 2015 ‐ has brought the number of validly named species of 112 Lactobacillus and Pediococcus to 273 (Figure 1 and Table S1), thus further increasing the diversity that 113 is associated with the genus Lactobacillus. The current taxonomy, although widely accepted by 114 medical community, food and health‐related industries, by lay‐persons, and used in national and 115 international regulations, impedes research aimed at understanding the ecology, , 116 evolution and applications of this important group of organisms. This is because micro‐organisms that 117 are genetically very distinct and metabolically, ecologically, and functionally very diverse are grouped 118 within the same genus. The lack of refined taxonomic structure, moreover, encourages the addition 119 of new species to a genus that has already been shown to be overly heterogeneous and prevents the 120 detection and description of functional properties or other communalities shared between members 121 of the subgroups. However, a proposal for a formal re‐evaluation of the taxonomy of the genera 122 Lactobacillus and Pediococcus has not been made so far. 123 Here we re‐evaluate the genetic relatedness and phylogeny of the species within the present genus 124 Lactobacillus and its sister taxa in the Lactobacillaceae and Leuconostocaceae through a polyphasic 125 approach [19]. For this, we considered Average Nucleotide Identity (ANI), Average Amino Acid Identity 126 (AAI) and core‐gene Average Amino Acid Identity (cAAI), core genome phylogeny, signature genes, 127 and metabolic or ecological criteria. Within the Lactobacillaceae, 26 lineages were identified that are 128 reliably separated and are characterised by conserved phenotypes and clade‐specific signature genes. 129 Twenty‐three of these clades are described here as new genera, the description of the genera 130 Lactobacillus and Paralactobacillus is emended while the description of the genus Pediococcus 131 remains unchanged. Furthermore, data of the present study demonstrate that the family 132 Leuconostocaceae Schleifer 2010 should be considered a later synonym of the family Lactobacillaceae 133 Winslow et al. 1917 (Approved Lists 1980). 134 METHODS 135 Phylogenomic re‐evaluation with RAxML and genome sequences of type strains 136 Genome sequences for type stains of all species in the families Lactobacillaceae and Leuconostocaceae 137 which were available on August 19th, 2019 were obtained from Genbank (Genome set 1; Table S1). A 138 listing of all species in the Lactobacillaceae is also available on https://site.unibo.it/subcommittee‐ 139 lactobacillus‐bifidobacterium/en and http://lactobacillus.ualberta.ca; the file hosted on the websites 140 will be periodically updated by adding new species that have been validly published. All genomes were 141 reannotated by Prokka [20], which uses Prodigal [21] for gene prediction. sequences for each 142 genome were extracted for gene clustering. FastOrtho was used to generate gene families based on 143 protein sequences. First, an all‐against‐all alignment was performed by Blastp [22] with an E‐value 144 cutoff of 10‐10. Then, ortholog groups were created with the MCL algorithm with an inflation value of 145 2. The clustering results were filtered by a local Perl script as previously described [14] to reduce the 146 influence of the fragmented protein sequences. All of the 114 single‐copy core gene families of 147 Lactobacillaceae and Leuconostocaceae were used for phylogenetic analysis. Protein sequences of 148 each family were aligned by Muscle [23]. All the 114 alignments were trimmed with TrimAl [24] and 149 were concatenated into a new alignment through a local Perl script. RAxML [25] was used for 150 phylogenetic analysis based on the core gene alignment with PROTGAMMAILGF (LG+I+G+F) as the 151 substitution model and 500 bootstrap samplings. The phylogenetic tree was visualized with iTOL [26]. 152 Phylogenomic re‐evaluation with iqtree and best quality genomes 153 A second tree of Lactobacillaceae and Leuconostocaceae species was calculated by using one 154 representative genome per species (Genome set 2) as described earlier [10]. Of the 2459 high‐quality 155 genomes analysed, 16 genomes could not be assigned to a known species owing to low whole‐genome

4

156 similarity or low 16S rRNA gene similarity to type strains; we labeled these species as “unassigned 157 species”. In addition, multiple outgroups were added. To select outgroups, we used the Genome 158 Taxonomy Database [27] to filter for the best quality genome for each of the 50 genera belonging to 159 the order Lactobacillales (excluding species of Lactobacillaceae and Leuconostocaceae), as evaluated 160 by CheckM completeness values. Potential outgroups with more than 5% estimated contamination 161 were excluded. The list of genomes used in the analysis is shown in Table S2. Genes were predicted 162 for ingroup and outgroup genomes with Prodigal version 2.6.3 [21]. Single‐copy core genes were 163 extracted using progenomics version 0.1.0 [28] with the following options: 30 seed genomes, 164 minimum presence in 25 seed genomes, and required single‐copy presence in 99% of all genomes. 165 Core genes were aligned using mafft version v7.407 [29]. The aligned core genes were then 166 concatenated into a protein supermatrix, and columns with more than 10% gaps were removed using 167 trimal version 1.4.rev15 [24]. A phylogeny was inferred on the supermatrix with iqtree version 1.6.11 168 [30], using the LG+G+F protein substitution model. Branch support was calculated using 1000 169 bootstrap trees with the UFBoot2 algorithm [31]. Finally, the full tree was rooted using the clade 170 (, Listeria_A, Brochothrix) as outgroup. The tree was visualized using ggtree version 1.16.0 [32]. 171 Calculation of average amino acid identity (AAI) and average amino acid identity of core 172 (cAAI) 173 AAI was calculated between each pair of type strain genome sequences (Genome set 1) using 174 CompareM [33]. cAAI values were additionally calculated to minimize the impact of horizontal gene 175 transfer on pairwise AAI values. Acquisition of genes by lateral gene transfer substantially contributes 176 to genetic diversity in bacteria [34]. The extent of gene acquisition by lateral gene transfer depends 177 on the lifestyle of the micro‐organism [35]. Lateral gene transfer distorts the molecular clock of 178 bacterial evolution and the inferred phylogenetic relationship between different species [36], 179 particularly for micro‐organisms that share a habitat and evolve by acquisition of similar genes. To 180 minimize the impact of lateral gene transfer, we defined the cAAI based on the protein sequences of 181 core gene families. We used soft core gene families that are shared by more than 90% of the genomes 182 studied. Protein sequences belonging to the soft‐core gene families of each genome were used to 183 caculate cAAI by CompareM. Differences between cAAI and AAI indicate divergent or convergent 184 evolution through acquisition of diverse or common genes, respectively. In addition, habitat 185 by specific phylogenetic clades was assessed by analysis of clade‐specific genes as 186 described below. 187 Identification of genes that are exclusive to specific phylogenetic clades (signature genes) 188 The complete pangenome of all best‐quality genomes (Genome set 2) was inferred using OrthoFinder 189 2.3.3 [37] with MMseqs2 version d36de [38] as sequence search program. For the analysis of gene 190 family presence/absence and signature genes, the outgroup genomes were removed from the tree 191 and the pangenome dataset. The gene family presence/absence plot was created by grouping 192 together gene families with the same presence/absence pattern across species, leaving out two types 193 of trivial patterns: gene family presence in a single species and gene family presence in all species. The 194 patterns with a frequency (number of gene families) of four or more were then visualized in 195 descending order of frequency. Signature genes were defined as gene families present in all genomes 196 of a clade (subtree) and absent in all other genomes. Phylogroups were defined by their type species; 197 species were assigned to the phylogroup of the type species they shared the most recent common 198 ancestor with. 199 For all analysis involving the core genome phylogenetic tree and the gene family presence/absence 200 patterns, R version 3.6.1 (https://www.R‐project.org) was used for data processing and visualization. 201 R packages that were crucial included the tidyverse version 1.2.1 (https://CRAN.R‐

5

202 project.org/package=tidyverse) and tidygenomes version 0.1.2 [39]. The code used for these analyses 203 is deposited in two repositories on GitHub [40]. 204 RESULTS 205 Phylogenomic evaluation of Lactobacillaceae 206 A core genome phylogenetic tree of all Lactobacillaceae type strains for which genome sequence data 207 was available in August 2019 is shown in Figure 2. The Lactobacillaceae consistently form 26 208 phylogenetic groups that match all prior core‐genome phylogenetic analyses of the family although 209 more than 60 genomes were added since 2015 [13, 14, 16, 17] and are supported with 100% bootstrap 210 values, indicating they have been shaped by cohesive evolutionary forces. Below, we propose genus 211 status for each of these 26 phylogenetic groups, which include an emended genus Lactobacillus (for 212 the phylogenetic group that includes L. delbrueckii, the type species of Lactobacillus), 213 Paralactobacillus, Pediococcus and 23 new genera consisting of species previously assigned to the 214 genus Lactobacillus. 215 The L. delbrueckii group that contains the type strain of the genus forms a monophyletic clade with L. 216 floricola and L. amylophilus. Heterofermentative lactobacilli together with pediococci and the L. 217 plantarum group also form a monophyletic clade; the remaining homofermentative lactobacilli, 218 however, are not monophyletic (Figure 2). Virtually all of the Lactobacillus species that were described 219 over the past 2 years cluster within one of the phylogenetic groups identified in 2017 (Figure 2)[17]. 220 Of the recently described species, only the candidate species Lactobacillus jinshani [41] can not be 221 assigned to one of the established phylogenetic groups and forms a separate lineage that is currently 222 represented by only this candidate species. 223 We have previously shown that the lifestyle of species within groups, as inferred from isolation source, 224 genomic, functional, ecological, and physiological information, is remarkably conserved within these 225 groups and can be assigned to insect or flower‐associated habitats, vertebrate hosts, to a free‐living 226 lifestyle, or to a nomadic lifestyle that transitions between different habitats [17]. For example, the L. 227 mali group that predominantly includes micro‐organisms with a free‐living lifestyle clusters separately 228 from the L. salivarius group, which predominantly includes micro‐organisms with a vertebrate host‐ 229 adapted lifestyle [17, 27](Figure 2). New species that were described since 2017 all conform to the 230 lifestyle that was assigned to other species in the same phylogenetic tree (Figure 2)[17]. 231 Evaluation on basis of cAAI and AAI values. 232 To validate the assumption that each of these 26 phylogenetic groups in the Lactobacillaceae 233 encompass a phylogenetic diversity that is commonly assigned to a bacterial genus, all 38,364 pairwise 234 cAAI and AAI values for the Leuconostocaceae and Lactobacillaceae species for which genome 235 sequences of the type strains were available were calculated (Table S3 and Table S4). The intra‐family 236 cAAI and AAI values for Lactobacillaceae, which are largely shaped by intra‐genus cAAI values of 237 Lactobacillus species, overlap with the inter‐family cAAI and AAI values for Lactobacillaceae and 238 Leuconostocaceae, confirming the phylogenetic heterogeneity of Lactobacillus as well as the lack of a 239 clear speration between Lactobacillaceae and Leuconostocaceae (Figure 3 and Figure S1). If intra‐ 240 group cAAI and AAI values are calculated for the 26 phylogenetic groups of Lactobacillaceae excluding 241 Pediococcus species, the distribution of intra‐group cAAI and AAI values matched the intra‐genus 242 distribution observed in Pediococcus, Weissella, and Leuconostoc (Figure 4 and Figure S2). Inter‐genus 243 cAAI values of more than 70% are observed for the L. brevis and L. collinoides groups. Despite these 244 relatively high cAAI values, the assignment of the L. brevis group and the L. collinoides group is justified 245 on the basis of the consistent clustering in phylogenetic trees (Figure 2) and the distinct metabolism 246 and ecology of species in the L. brevis and L. collinoides groups. Likewise, the description of the genus

6

247 Convivina despite high AAI values to Fructobacillus was based on ecological and metabolic criteria 248 Fructobacillus [42]. 249 The intra‐group distribution of cAAI and AAI values is shown in Figure 5 and Figure S3. With the 250 exception of the L. brevis, L. collinoides, L. reuteri and L. salivarius groups, all groups are exclusive, i.e. 251 the lowest intra‐group cAAI values are higher than the highest inter‐group cAAI values for any species 252 in the group (indicated in red in Figure 5; data provided in Table S3). The L. delbrueckii group, the L. 253 casei group and the L. salivarius group are among the most diverse groups. The diversity within the L. 254 casei and the L. salivarius groups relative to other groups is higher on the basis of AAI values (Figure 255 S3) than when assessed on the basis of cAAI values (Figure 5). This implies that the diversification of 256 the species in these groups is mediated by horizontal gene transfer and acquisition of lifestyle‐ 257 associated genes (see below). This observation matches the diverse lifestyles in the L. salivarius group, 258 which contains free‐living species or species with unknown lifestyle in addition to host‐adapted 259 species. Information on the ecology of the divergent L. pantheris / L. sharpeae clade within the L. casei 260 group is currently too limited to conclude on the lifestyle of these organisms. 261 Identification of genes that are exclusive to specific phylogenetic clades (signature genes) 262 To determine whether the 26 phylogenetic groups can be characterized by clade‐specific genes, we 263 analyzed the presence/absence of gene families within all species of the families Lactobacillaceae and 264 Leuconostocaceae [43]. Gene families that are present in all best‐quality genomes of a certain clade 265 but are absent in all other genomes were termed signature genes. Signature genes reflect a common 266 evolutionary history of a phylogenetic clade or result from horizontal gene transfer and relate to 267 common lifestyles, ecologies, and physiological properties. Signature genes therefore allow inferences 268 about the evolutionary forces that likely shaped the cluster. 269 Most of the proposed new genera are supported by signature genes. This is especially the case for the 270 L. delbrueckii, L. alimentarius, L. mellifer, L. concavus, L. perolens, L. sakei, L. coryniformis, L. casei, L. 271 plantarum, L. rossiae, L. vaccinostercus, L. kunkeei, L. fructivorans and L. brevis groups. Each of these 272 phylogroups contain at least four signature genes (Figure 6, Table S5). The genera Leuconostoc, 273 Fructobacillus, Oenococcus, Weissella and Pediococcus also show a relatively large number of 274 signature genes. Of the remaining groups, signature genes can be identified if the most distant 275 member(s) of the group is (are) omitted (Figure 2). The L. buchneri group contains signature genes if 276 L. senioris is omitted and the L. collinoides group contains signature genes if the L. malefermentans / 277 L. oryzae outgroup is omitted. The L. reuteri, L. salivarius, and L. mali groups do not contain signature 278 genes and can also not be divided into sub‐clades that contain signature genes (Fig. 6). Of note, the L. 279 reuteri group and the L. salivarius group were also identified as non‐exclusive on the basis of cAAI 280 values (Fig. 5). The remaining six phylogroups contain only one genome, making it impossible to assess 281 their harbouring of signature genes. Although phylogroups with a smaller number of species obviously 282 show larger numbers of signature genes, the impact of phylogroup sample size is limited. Even large 283 phylogroups such as the L. delbrueckii and L. alimentarius groups show a relatively large number of 284 signature genes. The identification of signature genes thus conforms to the phylogenetic analyses (Fig. 285 2) and cAAI values (Fig. 5), likely reflecting a common evolutionary history of phylogroups/genera, and 286 is therefore suitable to provide additional information on the delineation of bacterial genera. The 287 current signature genes analysis supports most of the new genera proposed in this work, particularly 288 the separation of the L. brevis and L. collinoides groups, which were combined in earlier studies [16, 289 27], and the separation of the L. salivarius and L. mali groups, which were also assigned to a single 290 phylogenetic group in the past [11, 13, 14]. 291 Phylogenomic evaluation of Lactobacillaceae and Leuconostocaceae

7

292 We further used the phylogenetic trees and cAAI values to explore the relationships of 293 Lactobacillaceae and Leuconostocaceae. To identify clades and nodes that are consistently identified 294 by different approaches, we deliberately used two different datasets, type strain genomes and best‐ 295 quality genomes, and different bioinformatics pipelines. The overall topology of the phylogenetic trees 296 was remarkably consistent. However, the core genome phylogenetic tree generated using the type 297 strains of the 26 phylogenetic groups of the Lactobacillaceae, 31 type strains of other genera in the 298 Lactobacillales, and 8 type strains from Bacillales as outgroup placed the Leuconostocaceae as a 299 monophyletic cluster within the Lactobacillaceae that shares the root with heterofermentative 300 lactobacilli, the genus Pediococcus, and the L. plantarum group (Figure 7A). The core genome tree 301 based on the genome set used for the signature gene analysis (best‐quality genomes) placed the 302 Leuconostocaceae as a monophyletic cluster within the heterofermentative lactobacilli, sharing the 303 root with the L. rossiae, L. reuteri and L. vaccinostercus groups (Figure 7B and Figure S4). This means 304 that the family Lactobacillaceae is not monophyletic unless Leuconostocaceae are included. The close 305 relationship of Leuconostocaceae and Lactobacillaceae is also supported by the cAAI values (Figure 8 306 and Table S3). Inter‐family cAAI and AAI values between Leuconostocaceae and Lactobacillaceae 307 overlap with the intra‐family cAAI values. Moreover, the cAAI values between Leuconostocaceae and 308 heterofermentative lactobacilli (Table S3) range from 53 to 60% and are thus in the same range as the 309 cAAI values between heterofermentative lactobacilli and the L. delbrueckii group (54% to 58%). These 310 findings do not support a taxonomic separation of the two families. 311 DISCUSSION 312 Family‐level considerations. The genus Pediococcus has consistently been recognized as an integral 313 part of the genus Lactobacillus. Some studies also suggested that the family Leuconostocaceae, which 314 was described in in 2010 on the basis of 16S rRNA sequence similarities [1, 44], are, on the contrary, 315 an integral part of the lactobacilli [15, 16]. The phylogenetic and comparative genomic analyses 316 conducted here confirmed that Leuconostocaceae and Lactobacillaceae are closely related and 317 intertwined. Moreover, two different datasets and bio‐informatic approaches placed the 318 Leuconostocaceae as a monophyletic cluster within the Lactobacillaceae. This result is also in line with 319 the Genome Taxonomy Database (https://gtdb.ecogenomic.org/, 24), in which the members of the 320 Leuconostocaceae were considered as members of the Lactobacillaceae. 321 The current analyses also indicate that heterofermentative lactobacilli are more closely related to 322 Leuconostoc and Weissella than they are to the L. delbrueckii group (Figure 8, Table S2 and S3). This 323 confirms that the two types, homofermentative and heterofermentative, are closely 324 linked to the phylogeny of lactobacilli. The genetic relatedness between heterofermentative 325 lactobacilli and Leuconostocaceae as assessed on the basis of cAAI values is closer than the 326 relationship between heterofermentative lactobacilli and the L. delbrueckii group. Exceptions are 327 Oenococcus species, which share less than 54.5% cAAI to any current member of the Lactobacillaceae. 328 Despite the overall congruent topology, the phylogenetic trees generated in this study are inconsistent 329 with respect to the position of Leuconostocaceae within the Lactobacillaceae. Depending on the 330 dataset used for calculation of the tree, the root of Leuconostocaceae is shared with all 331 heterofermentative lactobacilli, Pediococcus and the L. plantarum group (Figure 7A), or shared with 332 the L. reuteri, L. vaccinostercus and the L. rossiae group only (Figure 8 and Figures S4 and S5) [16]. All 333 of these trees support the observation that L. iners and Oenococcus species are the most distantly 334 related members of Lactobacillaceae and Leuconostocaceae, respectively, with respect to their cAAI 335 values (50.58%). The uncertainty with respect to the last common ancestor of Leuconostocaceae and 336 Lactobacillaceae has no implications for their taxonomic assignment into a single family. As each node 337 separating homofermentative from heterofermentative lactic acid bacteria represents a switch of a

8

338 micro‐organism from homofermentation to heterofermentation, however, it relates to the molecular 339 and ecological evolution of lactic acid bacteria and may thus be of interest for future studies. 340 Within Lactobacillaceae, the L. delbrueckii group forms a robust monophyletic clade with the L. 341 floricola group and the L. amylophilus group. Species in this clade also differ from other lactobacilli 342 with regards to physiological criteria, e.g. vancomycin sensitivity related to the inter‐peptide of the 343 peptidoglycan, the absence of pyruvate formate lyase, and the absence of the pentose‐phosphate 344 pathway enabling homofermentative pentose metabolism [14, 45]. The L. mellifer group and the L. 345 alimentarius group represent the link between the L. delbrueckii group and other lactobacilli with 346 respect to phylogeny and phenotypes; Pediococcus and the L. plantarum group represent the 347 evolutionary link between homofermentative and heterofermentative lactic acid bacteria. Although 348 pediococci and the L. plantarum group obviously share major metabolic features with 349 homofermentative lactobacilli [18], they are phylogenetically related to heterofermentative 350 lactobacilli and Leuconostocaceae (this study). 351 Criteria for delineation of new genera. Considerations of the different forces that shape bacterial 352 evolution led to the proposal of a methods‐free concept in bacterial taxonomy that considers 353 ecological divergence rather than numerical thresholds [6]. For species level taxonomy, the ANI 354 between two genomes has been consistently used to delineate new taxa, however, the phylogenetic 355 signal of ANI values is lost for ANI values below 70%, i.e. ANI is not a useful metrics for genus level 356 taxonomy. This was particularly noted for the taxonomy of genus Lactobacillus [14, 16]. The pairwise 357 average amino acid identity (AAI) and the conserved proteins (POCP) have been proposed for 358 classification at the genus level [5, 46]; of these two, the AAI is the more powerful metrics because it 359 is based on the proteins sequences and does not only account for the presence or absence of protein. 360 Although formal thresholds for genus‐level AAI values have not been established, the vast majority 361 bacterial intra‐genus AAI values is higher than 68 % [5]. Moreover, AAI values can be calculated on the 362 basis of core proteins to exclude proteins that were acquired by lateral gene transfer (this study), an 363 approach that was also employed for comparison on the basis of nucleotide identities [10]. Threshold 364 values for the delineation of new bacterial genera on the basis of AAI or cAAI values have not been 365 consistently used [43] but the transition zones for intra‐genus and inter‐genus AAI and cAAI values can 366 be derived by comparison with other bacterial genera, or alternative taxonomic approaches [27]. A 367 framework for taxonomy of isolates with unknown ecology including uncultured organisms was 368 previously established on the basis of the relative evolutionary distance of bacteria as determined by 369 core genome phylogeny [27]. This Genome Taxonomy Database classified species of the genus 370 Lactobacillus into 18 phylogenetic clades equivalent to genera which overlap with the 24 phylogenetic 371 clades that were proposed on the basis of ecological and phylogenetic considerations [14, 17]. An 372 approach focusing on ecology and evolution has also been applied to lactobacilli [17] and 373 demonstrated a remarkable overlap of their phylogeny and ecology. A methods‐free approach, 374 however, relies on information on the ecology of a multiple isolates of a specific bacterial taxon. 375 Currently, ecology and evolution are well‐studied for only a small subset of species in the genus 376 Lactobacillus, while the ecology of a large number of species and several phylogenetic groups remains 377 unclear because of the lack of data or the low number of species in the group [17]. Building on previous 378 studies on the taxonomy, ecology and phylogeny of Lactobacillus, we based the delineation of novel 379 genera on the following criteria, listed in decreasing order of priority: (i) the novel genera represent 380 monophyletic phylogenetic groups; (ii) intra‐genus AAI and cAAI values are higher than inter‐genus 381 AAI and cAAI values, and these show limited overlap; (iii) species in the proposed genera have common 382 characteristics with regard to ecology and physiology that differentiate the proposed genus from other 383 genera, and this distinction is generally supported by the presence signature genes [17, 43]; and (iv)

9

384 the proposed genera are largely consistent with the previously established phylogenetic groups [13, 385 14, 17] and with the classification based on relative evolutionary distance [27]. 386 Classification of the Lactobacillaceae species into 26 genera comprising an emended genus 387 Lactobacillus (i.e. one confined to the L. delbrueckii group), Pediococcus, Paralactobacillus, and 23 new 388 genera that correspond to the phylogenetic groups shown in Fig. 2 fits these four criteria best. The 389 proposed genera Lacticaseibacillus (the L. casei group) and Ligilactobacillus (the L. salivarius group) 390 remain relatively heterogeneous, particularly with respect to their AAI values, indicating that specific 391 subgroups in these genera currently adapt to different ecological habitats. This was proposed for the 392 L. casei group with respect to oxidative stress tolerance [47] and for the L. salivarius group where 393 megaplasmids and specific exopolysaccharide clusters may relate to human host adaptation [48]. 394 Conversely, the proposed genus Secundilactobacillus (the L. collinoides group) and the proposed genus 395 Levilactobacillus (the L. brevis group) are relatively homogeneous with respect to their cAAI values, 396 but they are separated by phylogenetic analysis, their metabolism, and their ecology. The L. collinoides 397 group is differentiated from L. brevis by adaptation to hexose‐depleted habitats, which is reflected by 398 lack of ‐dehydratase, diol‐dehydratase activity, and a metabolic focus on pentoses. These 399 metabolic and ecological differences are also supported by the more divergent AAI values and the 400 identification of signature genes. 401 Overall, the available evidence is highly consistent in its support with the proposed taxonomic 402 classification. Moreover, 16S rRNA sequence identities and AAI values readily allow new species to be 403 assigned to one of the 26 genera of Lactobacillaceae. Species that exhibit a 16S rRNA gene identity 404 that is greater than 94.5% to the type species of a genus [49] and cluster integral to that genus when 405 using 16S rRNA phylogeny are generally assigned correctly even in the absence of further analyses 406 (Fig. S6). However, 16S rRNA gene identity and 16S rRNA phylogeny should be complemented with 407 core genome phylogeny in combination with whole‐genome similarity metrics to validate the 408 taxonomy at the genus level [4]. We compared the performance of several whole‐genome metrics, 409 i.e. ANI, CNI, AAI and cAAI. Of these four, ANI and AAI can easily be computed using publicly available 410 tools. Novel species of Lactobacillaceae can be classified on the genus level using an AAI threshold of 411 68% to the type strain of the most closely related genus [5] (Fig. S3 and S7). Values below that level 412 require a more detailed analysis that also includes core genome phylogeny and cAAI values, and may 413 justify the description of novel genera when phylogenetic placement and AAI and cAAI values are 414 supported by metabolic and ecological criteria. We believe that this proposed taxonomy will facilitate 415 further research and discovery. The diversity of lactobacilli – the generic term remains useful to 416 designate organisms in all 25 genera that are currently classified as Lactobacillus species ‐ is likely 417 much greater than currently known as a majority of strains were isolated from humans, domesticated 418 animals, and food. Sampling of more diverse plant or environmental sources, and of wild animals will 419 likely extend our perspective on the phylogenetic and metabolic diversity of Lactobacillaceae. 420 Species‐level considerations.

421 TAXONOMIC IMPLICATIONS OF THE STUDY. 422 Principle 8 of the International Code of Nomenclature of states that each order or taxon 423 of a lower rank with a given circumscription, position, and rank can bear only one correct name, i.e. 424 the earliest that is in accordance with the Rules of this Code. Based on the data discussed above, we 425 consider the family Leuconostocaceae Schleifer 2010, which was circumscribed on the basis of 426 phylogenetic analyses of 16S rRNA sequences a later synonym of the family Lactobacillaceae Winslow 427 et al. 1917 (Approved Lists 1980). Below we propose an emended description of the Lactobacillaceae 428 family.

10

429 We further propose that the 23 phylogenetic groups and single lines of descent (Figure 2) represent 430 novel genera. The new taxa are described below and an emended description of the genera 431 Lactobacillus and Paralactobacillus are proposed. The new genera are described in an order that 432 reflects their phylogenetic relationships and recognizes the distinct phylogenetic position of 433 homofermentative and heterofermentative lactobacilli (Figures 2, 5, 6, 7 and 8). 434 The genome based analyses confirmed that the only strain of P. lolii that has been described, P. lolii 435 DSM 19927T, is a strain of P. acidilactici, with cAAI and AAI values to the P. acidilactici type strain of 436 99.4% and 98.1%, respectively [50] (Tables S3 and S4). P. lolii is thus a later synonym of P. acidilactici. 437 The genome‐based analyses also suggested that the two previously described subspecies of L. aviarius 438 should be elevated to species level. Lactobacillus aviarius was isolated from the intestine of chickens 439 in 1984 and two subspecies were recognised based on different sugar fermentation profiles: L. aviarius 440 subsp. aviarius does not ferment trehalose and cellobiose (while L. aviarius subsp. araffinosus does) 441 but metabolises , , melibiose and (while L. aviarius subsp. araffinosus does 442 not) [51]. The availability of the genome sequences of the type strains of both subspecies revealed 443 that they are only distantly related, which support that these two subspecies should be recognised as 444 different species. 445 Emended description of the family Lactobacillaceae 446 The emended family Lactobacillaceae is circumscribed on the basis of phylogenomic analyses reported 447 in the present paper, and includes all the genera previously included in families Lactobacillaceae 448 Winslow et al. 1917 (Approved Lists 1980) and Leuconostocaceae Schleifer 2010, i.e. Convivina, 449 Fructobacillus, Lactobacillus, Leuconostoc, Oenococcus, Paralactobacillus, Pediococcus and Weissella. 450 Cells are Gram‐positive, non‐sporeforming facultative or strict anaerobic bacteria. Cells are coccoid or 451 rod‐shaped, which may form chains, pairs or tetrads (genus Pediococcus). Main product of the 452 fermentative metabolism is lactate, and other products may be , , CO2, formate, or 453 succinate. Complex nutritional requirements for amino , peptides, nucleic acid derivatives, 454 vitamins, salts, fatty acids or fatty acid esters, and fermentable . Lactobacillaceae are 455 the only family in the Lactobacillales that includes homofermentative and heterofermentative micro‐ 456 organisms. 457 Type genus: Lactobacillus Beijerinck 1901 212 (Approved Lists). 458 HOMOFERMENTATIVE LACTOBACILLACEAE 459 EMENDED DESCRIPTION OF LACTOBACILLUS 460 Lactobacillus species are Gram‐positive, homofermentative, thermophilic and non‐sporeforming rods. 461 Most Lactobacillus species do not ferment pentoses and none of the organisms encode genes for the 462 pentose phosphate pathway or pyruvate formate lyase. The emended description of the genus 463 includes all organisms that were previously assigned to the L. delbrueckii group [17]. Lactobacillus 464 species are host‐adapted; the Lactobacillus melliventris clade (previously termed the Firm‐5 clade) is 465 adapted to social bees [52] while all other Lactobacillus species are adapted to vertebrate hosts. 466 Lactobacillus species ferment a relatively broad spectrum of carbohydrates and have the strain‐ 467 specific ability to ferment extracellular fructans, , or glycogen [53, 54]. The L. melliventris clade 468 species also ferment a wider range of carbohydrates when compared to insect‐adapted species in the 469 genera Apilactobacillus and Bombilactobacillus. In intestinal habitats, Lactobacillus species are 470 generally associated with heterofermentative lactobacilli. For specific examples, it was shown that 471 cohabitation of Lactobacillus species with heterofermentative lactobacilli is based on long‐term 472 evolutionary relationships in biofilms [55] and a complementary preference for sources [18,

11

473 56]. Many Lactobacillus spp. are able to ferment mannitol, which also reflects co‐habitation with 474 heterofermenters. The metabolic focus of L. delbrueckii on lactose [57] explains its dominance in 475 yoghurt and cheese but also relates to its presence in the intestine of suckling piglets 476 [54]. The genus Lactobacillus remains a relatively heterogenous genus with L. iners as the most distant 477 member. L. iners has the smallest genome size among all Lactobacillaceae, which reflects its strict 478 adaptation to the human vagina. 479 In addition to their relevance in intestinal and vaginal ecosystems, Lactobacillus species frequently 480 occur in dairy and cereal fermentations and are widely used as starter cultures for production of 481 fermented dairy products [58, 59]. 482 A phylogenetic tree of all species in the genus Lactobacillus is provided in Figure S6A. 483 The type species of the genus Lactobacillus is L. delbrueckii. Although the nomenclature of species in 484 the emended genus Lactobacillus remains unchanged, a list of species and a list of their properties is 485 provided below. 486 Lactobacillus delbrueckii 487 Lactobacillus delbrueckii ( delbrücki) (del.brueck’i.i. N.L. gen. n. delbrueckii, of Delbrück, named 488 for M. Delbrück, a German bacteriologist). 489 Type species of the genus Lactobacillus. Because of the high phenotypic and genotypic similarities 490 between L. delbrueckii, L. leichmannii, L. lactis and L. bulgaricus, only L. delbrueckii is retained as a 491 separate species. Both L. lactis and L. leichmannii are treated as L. delbrueckii subsp. lactis and L. 492 bulgaricus as L. delbrueckii subsp. bulgaricus [60]. All strains produce D(‐)‐ lactic acid. 493 Lactobacillus delbrueckii subsp. bulgaricus 494 Lactobacillus delbrueckii subsp. bulgaricus (bul.ga’ri.cus. N.L. masc. adj. bulgaricus, Bulgarian). 495 Strains of this subspecies were previously referred to as L. bulgaricus. L. delbrueckii subsp. bulgaricus 496 ferment to D(‐)‐ lactic acid and also metabolise , mannose and lactose, but not 497 [60, 61]. L. delbrueckii subsp. bulgaricus undergoes genome reduction which particularly relates to 498 loss or silencing of genes coding for metabolism of carbohydrates [57]. The genome size is 1.76 Mbp 499 and the mol% GC content of DNA is 49.9. 500 Isolated from yoghurt and cheese and an important starter cultures in the production of these foods 501 [58, 59] but also detected by culture‐independent methodology in the intestinal of suckling 502 piglets [54]. 503 The type strain is ATCC 11842T = CCUG 41390T = CIP 101027T = DSM 20081T = IFO (now NBRC) 13953T 504 = JCM 1002T = LMG 6901T = LMG 13551T = NCTC 12712T = VKM B‐1923T. 505 Genome sequence accession number: JQAV00000000. 506 16S rRNA gene accession number: CR954253. 507 Lactobacillus delbrueckii subsp. delbrueckii 508 Lactobacillus delbrueckii (del.bruec’ki.i. N.L. gen. n. delbrueckii, of Delbrück, named after M. Delbrück, 509 a German bacteriologist). 510 L. delbrueckii subsp. delbrueckii ferment glucose to D(‐)‐lactic acid and also metabolise sucrose, 511 fructose and mannose, but not lactose. Characteristics of the species/subspecies are provided by [61– 512 65]. The genome size is 1.75 Mbp and the mol% GC content of DNA is 49.9. 513 Isolated from vegetable source, sour grain mash and fermented grains.

12

514 The type strain is ATCC 9649T = CCUG 34222T = CIP 57.8T = DSM 20074T = IFO (now NBRC) 3202T = JCM 515 1012T = LMG 6412T = NCIMB 8130T (formerly NCDO 213) = NRRL B‐763T = VKM B‐1596T. 516 Genome sequence accession number: AZCR00000000. 517 16S rRNA gene accession number: AY773949. 518 Lactobacillus delbrueckii subsp. indicus 519 Lactobacillus delbrueckii subsp. indicus (in’di.cus. L. masc. adj. indicus, of India, Indian, referring to the 520 geographical origin of the strains). 521 Lactobacillus delbrueckii subsp. indicus metabolise sucrose, fructose, lactose and mannose, but is 522 unable to ferment and trehalose [66]. The genome size is 1.88 Mbp and the mol% GC content 523 of DNA is 49.5. 524 Isolated from a fermented dairy product dahi from India. 525 The type strain is NCC725T = CCUG 51390T = DSM 15996T = JCM 15610T = LMG 22083T. 526 Genome sequence accession number: AZFL00000000. 527 16S rRNA gene accession number: AY421720. 528 Lactobacillus delbrueckii subsp. jakobsenii 529 Lactobacillus delbrueckii subsp. jakobsenii (ja.kob.se’ni.i. N.L. gen. n. jakobsenii, of Jakobsen, named 530 after Mogens Jakobsen for his significant contributions in the field of food microbiology including 531 biodiversity, production and safety of African fermented foods and beverages). 532 Lactobacillus delbrueckii subsp. jakobsenii metabolise sucrose, maltose and trehalose but is unable to 533 ferment lactose [67]. The genome size is 1.75 Mbp and the mol% GC content of DNA is 50.3. 534 Isolated from dolo wort used in the production of the fermented African beverge dolo in Burkina Faso. 535 The type strain is ZN7a‐9T=DSM 26046T = LMG 27067T. 536 Genome sequence accession number: JQCG00000000. 537 16S rRNA gene accession number: ALPY00000000. 538 Lactobacillus delbrueckii subsp. lactis 539 Lactobacillus delbrueckii subsp. lactis (lac’tis. L. gen. n. lactis, of milk). 540 L. delbrueckii subsp. lactis includes strains previously designated as L. lactis and L. leichmannii; L. 541 delbrueckii subsp. lactis ferment glucose to D(‐)‐lactic acid and also metabolises sucrose, fructose and 542 mannose, maltose and trehalose [60]. The genome size is 1.87 Mbp and the mol% GC content of DNA 543 is 49.9. 544 Isolated from milk, cheese, compressed and grain mash. 545 The type strain is L 110T = ATCC 12315T = CCUG 31454T = CIP 101028T = DSM 20072T = JCM 1248T = 546 LMG 7942T = NBRC 102622T = NRRL B‐4525T. 547 Genome sequence accession number: AZDE00000000. 548 16S rRNA gene accession number: AY050173. 549 Lactobacillus delbrueckii subsp. sunkii

13

550 Lactobacillus delbrueckii subsp. sunkii (sun’ki.i. N.L. gen. n. sunkii, of sunki, the name of the non‐salted, 551 traditional, Japanese pickle from which the type strain was isolated). 552 L. delbrueckii subsp. sunkii ferment glucose to D(‐)‐ lactic acid and also metabolise sucrose, fructose 553 and mannose, maltose but not lactose [68]. The genome size is 2.0 Mbp and the mol% GC content of 554 DNA is 50.1. 555 Isolated from a traditionally fermented Japanese red turnip. 556 The type strain is YIT 11221T = DSM 24966T = JCM 17838T. 557 Genome sequence accession number: CP018217. 558 16S rRNA gene accession number: AB641833. 559 Lactobacillus acetotolerans 560 Lactobacillus acetotolerans (a.ce.to.to’le.rans. L. neut. n. acetum vinegar; L. pres. part. tolerans 561 tolerating, enduring; N.L. part. adj. acetotolerans vinegar tolerating). 562 Lactobacillus acetotolerans produces DL‐lactic acid from glucose, mannose, fructose and trehalose but 563 not from , sucrose, lactose, melibiose and raffinose [69]. The genome size is 1.59 Mbp and 564 the mol% GC content of DNA is 36.3. 565 The species is part of the core microbiome of mash fermentations for production of grain liquor and 566 vinegar in China and Japan [58]; it was also isolated from other plant fermentations, silage, and from 567 the intestine of swine, ducks, and cattle. 568 The type strain is ATCC 43578T = CCUG 32229T = CIP 103180T = DSM 20749T = JCM 3825T = LMG 10751T 569 = NBI 3014T. 570 Genome sequence accession number: AYZC00000000. 571 16S rRNA gene accession number: M58801. 572 Lactobacillus acidophilus 573 Lactobacillus acidophilus (a.ci.do’phi.lus. N.L. neut. n. acidum acid; Gr. masc. adj. philos loving; N.L. 574 masc. adj. acidophilus acid‐loving). 575 Lactobacillus acidophilus produces DL‐lactic acid from cellobiose, galactose, lactose, maltose, 576 mannose, sucrose and trehalose, but not from mannitol [70–72]. Specific strains have been used as 577 . The genome size of the type strain is 1.95 Mbp and the mol% GC content of DNA is 34.6. 578 Isolated from the intestinal tract of humans and animals, human mouth, human vagina, 579 and wine. 580 The type strain is ATCC 4356T = CCUG 5917T = CIP 76.13T = DSM 20079T = IFO (now NBRC) 13951T = 581 JCM 1132T = LMG 9433T = LMG 13550T = NCTC 12980T = NRRL B‐4495T = VKM B‐1660T. 582 Genome sequence accession number: AZCS00000000. 583 16S rRNA gene accession number: AY773947. 584 Lactobacillus amylolyticus 585 Lactobacillus amylolyticus (a.my.lo.ly'ti.cus. Gr. neut. n. amylon starch; N.L. masc. adj. lyticus (from Gr. 586 masc. adj. lytikos) able to loosen; N.L. masc. adj. amylolyticus starch‐digesting). 587 Lactobacillus amylolyticus an grow up to 52°C with an optimum growth temperature between 45 °C 588 and 48°C. No growth occurs at 20°C. These bacteria produce DL‐lactic acid from glucose, fructose,

14

589 galactose, glucose, maltose, mannose, sucrose raffinose and melibiose. Neither acid nor gas are 590 produced from arabinose, cellobiose, lactose, mannitol, rhamnose, and trehalose [73]. The 591 genome size is 1.54 Mbp and the mol% GC content of DNA is 38.2. 592 Isolated from malt, mash, and unhopped wort in breweries but was also identified in sourdough and 593 tofu whey. 594 The type strain is LA 5T = CCUG 39901T = DSM 11664T = JCM 12529T = LMG 18796T. 595 Genome sequence accession number: AZEP00000000. 596 16S rRNA gene accession number: FR683095. 597 Lactobacillus amylovorus 598 Lactobacillus amylovorus (a.my.lo.vo’rus. Gr. neut. n. amylon starch, L. v. vorare to devour, N.L. masc. 599 adj. amylovorus starch‐devouring). The species includes strains that were previously designated as 600 Lactobacillus sobrius [74]. 601 Lactobacillus amylovorus produces both D(‐) and L(+) lactic acid and acid is produced from cellobiose, 602 fructose, galactose, glucose, maltose, mannose, sucrose, starch, and trehalose. Arabinose, melezitose, 603 melibiose, raffinose, rhamnose and ribose are not fermented. The ability to ferment starch and the 604 presence of an extracellular amylolytic are distinguishing characteristics [75]. Growth 605 maximum is 45 to 48°C. The genome size of the type strain is 2.02 Mbp and the mol% GC content of 606 DNA is 37.8. 607 The is a characteristic representative of swine intestinal microbiota [54, 76]; also 608 isolated from sourdough and cattle waste‐corn fermentation. 609 The type strain is ATCC 33620T = CCUG 27201T = CIP 102989T = DSM 20531T = JCM 1126T = LMG 9496T 610 = NCAIM B.01458T = NRRL B‐4540T. 611 Genome sequence accession number: AZCM00000000. 612 16S rRNA gene accession number: AY944408. 613 Lactobacillus apis 614 Lactobacillus apis (a’pis. L. gen. n. apis of/from a honey bee, the genus name of the true honey bee 615 Apis mellifera L., referring to the insect host of the first strains). 616 Lactobacillus apis cells produce L‐lactic acid from glucose. Growth is found under strictly anaerobic 617 and microaerophilic conditions. Produces acid from glucose, fructose, mannose and salicin, but not 618 from galactose, maltose, raffinose, cellobiose, sucrose and lactose [77]. The genome size is 1.70 Mbp 619 and the mol% GC content of DNA is 36.9. 620 Isolated from the stomach contents of honeybees (Apis mellifera L.). 621 The type strain is R4BT = CCM 8403T = LMG 26964T. 622 Genome sequence accession number: PDKP00000000. 623 16S rRNA gene accession number: KF386017. 624 Lactobacillus bombicola 625 Lactobacillus bombicola [bom.bi’co.la. L. masc. n. bombus a boom, a deep hollow noise, buzzing, also 626 the zoological genus name of the bumble bee; L. suf. –cola (derived from L. masc. or fem. n. incola 627 incola, inhabitant) dwelling, occurring in; N.L. masc. n. bombicola occurring in Bombus].

15

628 Lactobacillus bombicola produces only D(‐)‐lactic acid from glucose. It is capable of utilizing cellobiose, 629 ribose, glucose, fructose, mannose, and trehalose for growth an acid production, but not arabinose, 630 maltose, lactose, melibiose, and sucrose [42]. The genome size is 1.64 Mbp and the mol% GC content 631 of DNA is 34.6. 632 Isolated from the gut of a Bombus lapidarius bumble bee. 633 The type strain is H70‐3T = LMG 28288T = DSM 28793T. 634 Genome sequence accession number: NPNG00000000. 635 16S rRNA gene accession number: LK054485. 636 Lactobacillus colini 637 Lactobacillus colini (co.li’ni. N.L. gen. n. colini of Colinus, scientific name of bobwhites). 638 L. colini ferments a broad range of hexoses and but pentoses are not fermented. 639 Optimum growth is observed at 37°C and between pH 5.0 and 5.5 [78]. The mol% GC content of DNA 640 is 35.6. 641 Isolated from bobwhites, a ground‐dwelling bird [78]. 642 The type strain is 111144 L1T = DSM 101872T = KCTC 21086T. 643 Genome accession number: not available at time of publication. 644 16S rRNA gene accession number: KU161105. 645 646 Lactobacillus crispatus (cris.pa’tus. L. part. adj. crispatus curled, crisped, referring to morphology 647 observed original in broth media). 648 Lactobacillus crispatus is synonymous with Lactobacillus acidophilus group A2 of Johnson et al. [72]. 649 It produces DL‐lactic acid from glucose, cellobiose, fructose, galactose, lactose, maltose, mannose, 650 and sucrose [79–81]. Arabinose, mannitol, melezitose or rhamnose are not fermented. Grows equally 651 well at 37 and 45°C. The genome size is 2.06 Mbp and the mol% GC content of DNA is 36.6. 652 One of the predominant species found in the human female lower genital tract. Isolated from human 653 feces, vagina, and buccal cavities, from crops and caeca of chicken and from patients with purulent 654 pleurisy, leucorrhea and urinary tract infections. Also isolated from type II . 655 The type strai is VPI 3199T = ATCC 33820T = CCUG 30722T = CIP 102990T = CIPP IIT = DSM 20584T = JCM 656 1185T = LMG 9479T. 657 Genome sequence accession number: AZCW00000000. 658 16S rRNA gene accession number: AF257097. 659 Lactobacillus equicursoris 660 Lactobacillus equicursoris (e.qui.cur’so.ris. L. masc. n. equus a horse; L. gen. n. cursoris of a runner or 661 racer; N.L. gen. n. equicursoris of a racing horse, referring to the isolation of the type strain from faeces 662 of a thoroughbred racehorse). 663 L. equicursoris produces D(‐)‐ lactic acid from glucose. It utilises glucose, fructose, galactose, mannose, 664 cellobiose, lactose and mannitol for growth and acid production [82]. The genome size is 2.05 Mbp 665 and the mol% GC content of DNA is 47.7. 666 Isolated from a thoroughbred racehorse.

16

667 The type strain is DI70T = DSM 19284T = JCM 14600T. 668 Genome sequence accession number: AZDU00000000. 669 16S rRNA gene accession number: AB290830. 670 Lactobacillus fornicalis 671 Lactobacillus fornicalis (for.ni.ca ́lis. N.L. masc. adj. fornicalis, of the posterior fornix). 672 L. fornicalis produces DL‐ lactic acid from glucose. Acid is produced from ribose, fructose, galactose, 673 glucose, mannose, maltose, cellobiose, sucrose, trehalose, melezitose, mannitol and sorbitol [83]. The 674 mol% GC content of DNA is 37. 675 Isolated from the human posterior vaginal fornix. 676 The type strain is TV 1018T = DSM 13171T = ATCC 700934T. 677 Genome sequence accession number: not available at the time of publication. 678 16S rRNA gene accession number: Y18654. 679 680 Lactobacillus gallinarum (gal.li.na'rum. L. gen. pl. n. gallinarum of hens). 681 Lactobacillus gallinarum produce DL‐lactic acid. Acid is produced from glucose, mannose, galactose, 682 sucrose, fructose, cellobiose, melibiose, and raffinose. No acid formation from arabinose, rhamnose, 683 ribose, trehalose, and mannitol. Synonymous with Lactobacillus acidophilus group A4 of Johnson et 684 al. [72]. Strains are tolerant to 4.0% NaCl. [72, 84]. The genome size of the type strain is 1.94 Mbp and 685 the mol% GC content of DNA is 36.5. 686 Isolated from the chicken intestine. 687 The type strain is L917, ScavT = ATCC 33199T= CCUG 30724T = CIP 103611T = DSM 10532T = JCM 2011T 688 = LMG 9435T = VPI 1294T. 689 Genome sequence accession number: AZEL00000000. 690 16S rRNA gene accession number: AJ417737. 691 692 Lactobacillus gasseri (gas’se.ri. N.L. gen. n. gasseri, of Gasser, named for F. Gasser, a French 693 bacteriologist). 694 Lactobacillus gasseri strains are all positive for glucose, mannose, galactose, maltose, sucrose and 695 fructose fermentation and produce DL‐lactic acid. Strains do not ferment ribose, mannitol and 696 raffinose. Further characteristics are provided by [84–86]. The genome size is 1.89 Mbp and the mol% 697 GC content of DNA is 35.3. 698 One of the predominant species in the human female lower genital tract. Also isolated from the human 699 mouth, intestinal tract, and from the intestine of animals. Also found in wounds, urine, blood, carious 700 dentine, and pus of patients suffering from septic infections. . 701 The type strain is 63 AMT of Gasser = ATCC 33323T = CCUG 31451T = CIP 102991T = DSM 20243T = JCM 702 1131T = LMG 9203T = NRRL B‐14168T = NRRL B‐4240T. 703 Genome sequence accession number: NC_008530. 704 16S rRNA gene accession number: AF519171.

17

705 Lactobacillus gigeriorum 706 Lactobacillus gigeriorum (gi.ge.ri.o‘rum. L. gen. pl. n. gigeriorum of or from the entrails or gizzards of 707 poultry). 708 Lactobacillus gigeriorum produces mainly D‐lactic acid from glucose, fructose, mannose, maltose, 709 sucrose, galactose and cellobiose. Ribose, mannitol, lactose and raffinose are not fermented [87]. 710 The genome size is 1.91 Mbp and the mol% GC content of DNA is 36.9. 711 Isolated from a crop of a chicken. 712 The type strain is 202T = LEM 202T = CRBIP 24.85T = DSM 23908T. 713 Genome sequence accession number: AYZO00000000. 714 16S rRNA gene accession number: FR681899. 715 Lactobacillus hamsteri 716 Lactobacillus hamsteri (ham’ste.ri. N.L. gen. n. hamster of the hamster from which the isolate was 717 derived). 718 Lactobacillus hamsteri produces DL‐lactic acid from glucose, cellobiose, sucrose, mannitol, raffinose 719 and ribose. No acid produced from melizitose [88]. The genome size is 1.84 Mbp and the mol% GC 720 content of DNA is 35.1. 721 Isolated from the intestine of a hamster. 722 The type strain is Ha5F1T = ATCC 43851T= CCUG 30726T = CIP 103365T = DSM 5661T = JCM 6256T= LMG 723 10754T. 724 Genome sequence accession number: AZGI00000000. 725 16S rRNA gene accession number: AJ306298. 726 Lactobacillus helsingborgensis 727 Lactobacillus helsingborgensis (hel.sing.bor.gen’sis. N.L. masc. adj. helsingborgensis pertaining to 728 Helsingborg, the site of Lund University, Campus Helsingborg, Sweden, where the type strain was 729 characterized). 730 Lactobacillus helsingborgensis growth occurs at 15 to 50 °C and D(‐)‐lactic acid is produced as the end 731 product from hexose fermentation. Acid is produced during fermentation of glucose, mannose, 732 sorbose, sorbitol and sucrose, but not from maltose or lactose [89]. The genome size is 2.02 Mbp and 733 the mol% GC content of DNA is 36.4. 734 Isolated from the honey stomach of the honeybee A. mellifera mellifera, and from alfalfa silage. 735 The type strain is Bma5NT = DSM 26265T = CCUG 63301T. 736 Genome sequence accession number: JXJR00000000. 737 16S rRNA gene accession number: JX099553. 738 739 Lactobacillus helveticus (hel.ve’ti.cus. L. masc. adj. helveticus Swiss, referring to the isolation of the 740 type strain from Emmental [Swiss] cheese). 741 Lactobacillus helveticus produces DL‐lactic acid from glucose galactose, lactose, mannose, and 742 trehalose but not from cellobiose, mannitol, raffinose, and sucrose. L. helveticus [2, 90] is an earlier

18

743 heterotypic synonym of Lactobacillus suntoryeus [91]. The genome size of the type strain is 1.83 Mbp 744 and the mol% GC content of DNA is 36.8. 745 Part of the core microbiome of chicken [92] but was also isolated from sour milk, cheese starter 746 cultures and cheese, particularly Emmental and Gruyère cheeses, and in tomato pomace and silage. 747 The type strain is 12, Lh12T = ATCC 15009T = CCUG 30139T = CIP 103146T = DSM 20075T = IFO (now 748 NBRC) 15019T = JCM 1120T = LMG 6413T = LMG 13555T = NRRL B‐4526T. 749 Genome sequence accession number: AZEK00000000. 750 16S rRNA gene accession number: AM113779. 751 Lactobacillus hominis 752 Lactobacillus hominis (ho’mi.nis. L. gen. n. hominis of a human being). 753 Lactobacillus hominis produces acid from galactose, glucose, fructose, mannose, cellobiose, maltose, 754 lactose, sucrose, trehalose and raffinose. Mainly D‐lactic acid (about 90 %) is produced from glucose 755 [93]. The genome size is 1.93 Mbp and the mol% GC content of DNA is 35.2. 756 Isolated from the human intestine. 757 The type strain is 61DT = CRBIP 24.179T = DSM 23910T. 758 Genome sequence accession number: AYZP00000000. 759 16S rRNA gene accession number: FR681902. 760 761 Lactobacillus iners (in’ers. L. masc. adj. iners, inactive, lazy). 762 Lactobacillus iners grows on blood agar but not on MRS or Rogosa agar, reflecting a strict adaptation 763 to the human vagina. L( +)‐Lactic acid is produced from glucose, some strains produce acid from 764 maltose but acid is not produced from lactose, mannitol, raffinose, ribose, and sucrose [94]. The 765 genome size is 1.27 Mbp and the mol% GC content of DNA is 32.5. 766 One of the predominant species found in the human female lower genital tract; also occurs on human 767 skin [95] 768 The type strain is CCUG 28746T = CIP 105923T = DSM 13335T = JCM 12513T = LMG 18914T. 769 Genome sequence accession number: AZET00000000. 770 16S rRNA gene accession number: Y16329. 771 Lactobacillus intestinalis 772 Lactobacillus intestinalis (in.tes.tina’lis. N.L. masc. adj. intestinalis, pertaining to the intestine). 773 Lactobacillus intestinalis produce DL‐lactic acid from glucose, mannose, fructose, galactose, sucrose 774 and mannitol, but not from arabinose, , rhamnose, and trehalose [96]. The genome size is 2.01 775 Mbp and the mol% GC content of DNA is 35.4. 776 Isolated from the intestines of rats, mice, and pigs. 777 The type strain is Th4T = ATCC 49335T= CCUG 30727T = CIP 104793T = DSM 6629T = JCM 7548T = LMG 778 14196T. 779 Genome sequence accession number: AZGN00000000. 780 16S rRNA gene accession number: AJ306299.

19

781

782 Lactobacillus jensenii (jen.se’ni.i. N.L. gen. n. jensenii, of Jensen, named for S. Orla‐Jensen, a Danish 783 microbiologist). 784 Lactobacillus jensenii produces only the D(‐) lactic enantiomer. Cellobiose, sucrose and maltose 785 fermented; lactose, mannitol and arabinose not fermented [97]. The genome size is 1.61 Mbp and the 786 mol% GC content of DNA is 34.33. 787 One of the predominant species in the human female lower genital tract. 788 The type strain is 62GT = ATCC 25258T = CCUG 21961T = CCUG 35572T = CIP 69.17T = DSM 20557T = JCM 789 1146T = JCM 15953T = LMG 6414T = NRRL B‐4550T. 790 Genome sequence accession number: AYYU00000000. 791 16S rRNA gene accession number: AF243176. 792 793 Lactobacillus johnsonii (john.so'ni.i. N.L. gen. n. johnsonii of Johnson; named for J. L. Johnson, an 794 American microbiologist). Synonymous with L. acidophilus group B2 of Johnson et al. [72]. 795 Lactobacillus johnsonii strains all ferment glucose, mannose, galactose, maltose, sucrose and fructose 796 and produce DL‐lactic acid.L. johnsonii does not ferment mannitol or ribose [84]. The genome size is 797 1.77 Mbp and the mol% GC content of DNA is 34.4. 798 Isolated from humans (gut, vagina) and the feces of birds, rodents, calves and pigs, and from type II 799 sourdoughs. 800 The type strain is ATCC 33200T = CCUG 30725T = CIP 103620T = DSM 10533T = JCM 2012T = VPI 7960T. 801 Genome sequence accession number: AZCY00000000. 802 16S rRNA gene accession number: AJ002515. 803 Lactobacillus kalixensis 804 Lactobacillus kalixensis (ka.lix.en‘sis. N.L. masc. adj. kalixensis pertaining to Kalix, a town in northern 805 Sweden, where the gastric biopsies were sampled). 806 Lactobacillus kalixensis produces both D(‐)‐ and L(+)‐lactate from galactose, glucose, fructose, 807 mannose, cellobiose, maltose, lactose, sucrose, trehalose and raffinose. Acid is not produced 808 arabinose, ribose, xylose, rhamnose and mannitol [98]. The genome size is 2.08 Mbp and the mol% 809 GC content of DNA is 36.1. 810 Isolated from a biopsy of the healthy human gastric mucosa. 811 The type strain is Kx127A2T = CCUG 48459T = DSM 16043T = JCM 15954T = LMG 22115T. 812 Genome sequence accession number: AZFM00000000. 813 16S rRNA gene accession number: AY253657. 814 Lactobacillus kefiranofaciens 815 Lactobacillus kefiranofaciens (ke.fi.ra.no.fa'ci.ens. N.L. neut. n. kefiranum, a of 816 grain, kefiran; L. v. facio, produce; N.L. part. adj. kefiranofaciens, kefiran producing).

20

817 Lactobacillus kefiranofaciens produces DL‐lactic acid with an excess of D(‐)‐lactic acid from glucose, 818 fructose, galactose, sucrose, maltose, lactose, and raffinose, but not from arabinose, ribose, cellobiose 819 or trehalose [99]. 820 Two subspecies are recognised. 821 Lactobacillus kefiranofaciens subsp. kefiranofaciens 822 Lactobacillus kefiranofaciens subsp. kefiranofaciens (ke.fi.rano. fa'ci.ens. L. n. kefiran, a polysaccharide 823 of kefir grain, kefiran; L. v. facio, produce; N.L. part. adj. kefiranofaciens, kefiran producing). 824 The genome size of the type strain is 2.26 Mbp and the mol% GC content of DNA is 37.2. 825 Part of the microbiota of kefir grains [99, 100] but also isolated from other fermented dairy products. 826 The type strain is WT‐2BT = ATCC 43761T= CCUG 32248T = CIP 103307T = DSM 5016T = JCM 6985T = 827 LMG 19149T. 828 Genome sequence accession number: AZGG00000000. 829 16S rRNA gene accession number: AM113781. 830 Lactobacillus kefiranofaciens subsp. kefirgranum 831 Lactobacillus kefiranofaciens subsp. kefirgranum (ke.fir.gra’num. Turkish n. kefir, Caucasian sour milk; 832 L. n. granum grain; N.L. neut. n. kefirgranum kefir grain). 833 The genome size of the type strain is 2.10 Mbp and the mol% GC content of DNA is 37.5. 834 Part of the core microbiome of kefir grains [100, 101]. 835 The type strain is GCL 1701T = ATCC 51647T = CCUG 39467T = CIP 104241T = DSM 10550T = JCM 8572T 836 = LMG 15132T. 837 Genome sequence accession number: AZEM00000000. 838 16S rRNA gene accession number: AM113782. 839 Lactobacillus kimbladii 840 Lactobacillus kimbladii (kim.bla‘di.i. N.L. gen. n. kimbladii named after beekeeper Tage Kimblad, for 841 his significant contributions to the discovery of the LAB microbiota in the honey stomach of 842 honeybees). 843 Lactobacillus kimbladii grows at 15 to 50°C and D(‐)‐lactate from glucose, fructose, mannose and 844 tagatose, but not from ribose, sorbitol, cellobiose and lactose [89]. The genome size is 2.19 Mbp and 845 the mol% GC content of DNA is 36.0. 846 Isolated from the honey stomach of the honeybee A. mellifera. 847 The type strain is Hma2NT=DSM 26263T=CCUG 63633T. 848 Genome sequence accession number: JXLH00000000. 849 16S rRNA gene accession number: JX099549. 850 Lactobacillus kitasatonis 851 Lactobacillus kitasatonis (ki.ta.sa.to‘nis. L. gen. n. kitasatonis referring to Shibasaburo Kitasato, the 852 founder of Kitasato Institute, the father of Japanese bacteriology).

21

853 Lactobacillus kitasatonis produces DL‐lactic acid from mannose, maltose, galactose, sucrose and 854 fructose while acid is not produced from arabinose, xylose, ribose, trehalose, melibiose and raffinose 855 [102]. The genome size of the type strain is 1.91 Mbp and the mol% GC content of DNA is 37.5. 856 Isolated from the intestine of animals including chicken and swine. 857 The type strain is T. Mitsuoka Ch‐J‐2‐1T =JCM 1039T = KCTC 3155T. 858 Genome sequence accession number: AZFU00000000. 859 16S rRNA gene accession number: AB107638. 860 Lactobacillus kullabergensis 861 Lactobacillus kullabergensis (kul.la.ber.gen‘sis. N.L. masc. adj. kullabergensis of or belonging to the 862 nature reserve Kullaberg, where the discovery of these strains was made in 2005). 863 Lactobacillus kullabergensis grows at 15–50°C; D(‐)‐lactate is produced as the end product from 864 hexose fermentation. Acid is produced from glucose, fructose, trehalose and gentiobiose, but not from 865 ribose, galactose, mannose, maltose, lactose and sucrose [89]. The genome size is 2.12 Mbp and the 866 mol% GC content of DNA is 35.8. 867 Isolated from the honey stomach of the honeybee A. mellifera mellifera. 868 The type strain is Biut2NT=DSM 26262T=CCUG 63631T. 869 Genome sequence accession number: JXBY00000000. 870 16S rRNA gene accession number: JX099550. 871 Lactobacillus melliventris 872 Lactobacillus melliventris (mel.li.ven‘tris. L. neut. n. mel, mellis honey; L. masc. n. venter, ‐tris belly, 873 stomach; N.L. gen. n. melliventris of the honey stomach, referring to the isolation of the first strains 874 from the honey stomach of honeybees). 875 Lactobacillus melliventris grows from 15 to 50°C. Produce acid from glucose, fructose, mannose and 876 gentiobiose, but not from galactose, ribose, sucrose, maltose and lactose [89]. The genome size is 2.12 877 Mbp and the mol% GC content of DNA is 35.9. 878 Isolated from the homey stomach of honeybees. 879 The type strain is Hma8NT = DSM 26256T = CCUG 63629T. 880 Genome sequence accession number: JXLI00000000. 881 16S rRNA gene accession number: JX099551. 882 Lactobacillus mulieris 883 Lactobacillus mulieris (mu.li’.e.ris. L. gen. n. mulieris of a woman, from where the bacterium was 884 isolated). 885 Lactobacillus mulieris grows in the pH range of 5.0 ‐ 8.5 and from 30 to 45°C; optimum growth is 886 observed at 37°C [103]. Lactic acid is produced from glucose, fructose, mannose, N‐acetylglucosamine, 887 several disaccharides and starch but not from pentoses [103]. The genome size is 1.66 Mbp and the 888 mol% GC content of DNA is 34.2. 889 Isolated from the urine of a woman; several strains previously classified as L. jensenii should be 890 classified as L. mulieris [103].

22

891 The type strain is c10Ua161MT = CECT 9755T = DSM 108704T. 892 Genome sequence accession number: SDGL00000000. 893 16S rRNA gene accession number: MK775269. 894 Lactobacillus panisapium 895 Lactobacillus panisapium (pa.nis.a’pi.um. L. masc. n. panis bread; L. fem. n apis bee; N.L. gen. n. 896 panisapium of bee bread). 897 Lactobacillus panisapium is facultatively anaerobic but optimal growth is observed under anaerobic 898 conditions. Growth occurs from 15 up to 55°C (optimum 37°C) and it produces acid from cellobiose, 899 fructose, galactose, glucose, melibiose, ribose, sucrose, mannose and raffinose [104]. The genome size 900 is 1.83 Mbp and the mol% GC content of DNA is 37.4. 901 Isolated from bee bread of Apis cerana. 902 The type strain is Bb 2‐3T = DSM 102188T = ACCC 19955T. 903 Genome sequence accession number: NPNH01000000. 904 16S rRNA gene accession number: KX447147. 905 Lactobacillus paragasseri 906 Lactobacillus paragasseri (pa.ra.gas’se.ri. Gr. prep. para, resembling; N.L. gen. n. gasseri, a species 907 epithet; N.L. gen. n. paragasseri, resembling Lactobacillus gasseri). 908 Lactobacillus paragasseri produces both D(‐)‐ and L(+)‐lactic acid as end products of glucose 909 fermentation (75:25 ratio). Also ferments maltose, lactose, sucrose and trehalose, but not ribose and 910 raffinose [105]. The genome size is 1.94 Mbp and the mol% GC content of DNA is 34.9. 911 Occurs in the human . 912 The type strain is M. Rogosa 208XRT = JCM 5343T = ATCC 4963T = LMG 11478T = NCFB 1375T = KCTC 913 3172T = NCIMB 8931T = VPI 0334T. 914 Genome sequence accession number: AP018549. 915 16S rRNA gene accession number: LC374363. 916 Lactobacillus pasteurii 917 Lactobacillus pasteurii (pas.teu‘ri.i. N.L. gen. masc. n. pasteurii of Pasteur). 918 Lactobacillus pasteurii produces mainly D(‐)‐lactic acid from glucose; acid is also produced from ribose, 919 fructose, mannose, cellobiose, maltose, lactose and sucrose [93]. The genome size is 1.87 Mbp and 920 the mol% GC content of DNA is 38.5. 921 Isolated from the human intestine. 922 The type strain is 1517T = CRBIP 24.76T = DSM 23907T. 923 Genome sequence accession number: AYZN00000000. 924 16S rRNA gene accession number: FR681901. 925 Lactobacillus porci 926 Lactobacillus porci (por’ci. L. gen. n. porci of a pig, referring to the isolation of the type strain from 927 small intestine of a pig).

23

928 Lactobacillus porci grows between 15 and 50 °C and produces D(‐)‐lactic acid from glucose; acid is also 929 produced from mannose, cellobiose, maltose, lactose, trehalose, raffinose and sucrose [106]. The 930 mol% GC content of DNA is 51.5. 931 Isolated from the swine intestine.

T T T 932 The type strain is SG816 = KCTC 21090 = NBRC 112917 . 933 Genome sequence accession number: not available at the time of publication. 934 16S rRNA gene accession number: MF346092 935 Lactobacillus psittaci 936 Lactobacillus psittaci (psit.ta‘ci. L. gen. masc. n. psittaci of the parrot, from which the organism was 937 first isolated). 938 Lactobacillus psittaci produces acid from glucose, raffinose and sucrose, but not from lactose, 939 mannitol and trehalose [107]. The genome size is 1.54 Mbp and the mol% GC content of DNA is 35.6. 940 Isolated from a hyacinth macaw. 941 The type strain is B 1491/99T = CCUG 42378T = CIP 106492T = DSM 15354T = JCM 11552T.

942 Genome sequence accession number: AZFB00000000. 943 16S rRNA gene accession number: AJ272391. 944 Lactobacillus rodentium 945 Lactobacillus rodentium (ro.den‘ti.um. L. gen. pl. n. rodentium of gnawers, referring to the fact that 946 the microorganism was isolated from wild rodents). 947 Lactobacillus rodentium utilizes glucose, fructose, maltose, melibiose and sucrose, but not ribose, 948 mannitol or trehalose [108]. The genome size is 1.52 Mbp and the mol% GC content of DNA is 34.0. 949 Isolated from the colon of wild mice (Mus musculus) and other rodent species [55, 108]. 950 The type strain is MYMRS/TLU1T = DSM 24759T = CCM 7945T. 951 Genome sequence accession number: BFBY00000000. 952 16S rRNA gene accession number: HQ851022. 953 Lactobacillus taiwanensis 954 Lactobacillus taiwanensis (tai.wa.nen’sis. N.L. masc. adj. taiwanensis of Taiwan, referring to the origin 955 of the type strain). 956 L. taiwanensis produces both D and L lactic acid enantiomers from glucose fermentation. Fructose, 957 mannose, maltose, lactose, sucrose and trehalose are also fermented. No acid is produced from 958 raffinose or ribose [109]. The genome size is 1.88 Mbp and the mol% GC content of DNA is 34.0. 959 Occurs in the mouse gastrointestinal tract [55] but also isolated from silage cattle feed. 960 The type strain is FIRDI 006T = BCRC 17755T = DSM 21401T. 961 Genome sequence accession number: AYZG00000000. 962 16S rRNA gene accession number: EU487512.

24

963 Lactobacillus ultunensis 964 Lactobacillus ultunensis (ul.tun.en’sis. N.L. masc. adj. ultunensis pertaining to Ultuna, the site of 965 Swedish University of Agricultural Sciences in Uppsala, Sweden). 966 Lactobacillus ultunensis produces both D‐ and L‐lactate from glucose. Acid is produced from galactose, 967 fructose, mannose, cellobiose, maltose, lactose, sucrose, and trehalose. Acid is not produced from 968 arabinose, ribose, rhamnose and melezitose. Growth occurs at 42 but not at 45°C [98]. The genome 969 size of the type strain is 2.16 Mbp and the mol% GC content of DNA is 36.0. 970 Isolated from a biopsy of a healthy human gastric mucosa. 971 The type strain is Kx146C1T = CCUG 48460T = DSM 16047T = JCM 16177T = LMG 22117T. 972 Genome sequence accession number: AZFO00000000. 973 16S rRNA gene accession number: AY253660. 974 Lactobacillus xujianguonis 975 Lactobacillus xujianguonis (xu.jian.guo'nis. N.L. gen. masc. n. xujianguonis of Xu Jianguo, recognized 976 for contributions to medical microbiology). 977 Lactobacillus xujianguonis grows optimally at 37 – 40°C and at neutral pH [110]. DL‐lactic acid is 978 produced from pentoses, hexoses, disaccharides, sorbitol and mannitol. The genome size of the type 979 strain is 2.22 Mbp and the mol% GC content of DNA is 38.8. 980 Isolated from a Himalayan marmot (Marmota himalayana). 981 The type strain is HT111‐2T = CGMCC 1.13855T = KCTC 15803T. 982 Genome sequence accession number: RXIA00000000. 983 16S rRNA gene accession number: MK294239. 984 DESCRIPTION OF AMYLOLACTOBACILLUS GEN. NOV. 985 Amylolactobacillus (A.my.lo.lac.to.ba.cil’lus Gr. neut. n. amylon starch; N.L. masc. n. Lactobacillus a 986 bacterial genus); N.L. masc. n. Amylolactobacillus, a lactobacillus that ferments starch. 987 Strains of Amylolactobacillus are thin rods, (0.5–0.9 μm wide and 1.2–3 μm long) occurring singly and 988 in short chains, non‐motile, Gram‐positive, ‐ negative, oxidase‐negative, non‐‐forming. 989 Amylolactobacillus species are homofermentative and display extracellular amylolytic enzyme activity. 990 The mol% GC content is between 43.6 and 43.6. 991 The type species is Amylolactobacillus amylophilus; Amylolactobacillus was previously referred to as 992 L. amylophilus group. 993 Description of Amylolactobacillus amylophilus comb. nov. 994 Amylolactobacillus amylophilus (a.my.lo’phi.lus. Gr. neut. n. amylon starch; Gr. masc. adj. philos 995 loving; N.L. masc. adj. amylophilus starch‐loving). 996 Basonym: Lactobacillus amylophilus Nakamura and Crowell 1981, 216VP (Effective publication: 997 Nakamura and Crowell 1979, 539). 998 A. amylophilus strains ferment starch to L(+)‐lactic acid, they also metabolise fructose, galactose, 999 glucose, mannose and maltose [111]. The genome size is 1.56 Mbp. The mol% GC content of DNA is 1000 43.6 [111].

25

1001 Isolated from swine waste‐corn fermentation, corn‐starch processing industrial wastes and kocho 1002 (Ensete ventricosum) bread. 1003 The type strain is ATCC 49845T = LMG 6900T = DSM 20533T = CCUG 30137T = CIP 102988T = IFO (now 1004 NBRC) 15881T = JCM 1125T = NCAIM B.01457T = NRRL B‐4437T = NRRL B‐4476T. 1005 Genome sequence accession number: AYYS00000000. 1006 16S rRNA gene accession number: M58806. 1007 Description of Amylolactobacillus amylotrophicus comb. nov. 1008 Amylolactobacillus amylotrophicus (a.my.lo.tro’phi.cus. Gr. neut. n. amylon starch; N.L. masc. adj. 1009 trophicus from Gr. masc. adj. trophikos nursing, tending; N.L. masc. adj. amylotrophicus growing on 1010 starch, pertaining to the ability to ferment starch). 1011 Basonym: Lactobacillus amylotrophicus Naser et al. 2006, 2526VP. The classification of A. 1012 amylotrophicus as separate species was disputed as the first published genome sequence of the type 1013 strain of A. amylotrophicus was virtually identical to the sequence of A. amylophilus [14, 16]. The 16S 1014 rRNA, pheS and rpoA sequences provided with the new description, however, clearly differentiate A. 1015 amylotrophicus from A. amylophilus. 1016 Phenotypic properties that differentiate A. amylotrophicus from A. amylophilus include the 1017 production of acid from D‐cellobiose and salicin [112]. The mol% GC content of DNA is 43.6. 1018 Isolated from corn silage. 1019 The type strain is LMG 11400T = DSM 20534T = JCM 1124T = NRRL B‐4436T. 1020 Genome sequence accession number: not available at the time of publication. 1021 16S rRNA gene accession number: AM236149. 1022 DESCRIPTION OF HOLZAPFELIA GEN. NOV. 1023 Holzapfelia (Holz.ap.fe’li.a. N.L. fem. n. Holzapfelia, named after Wilhelm Holzapfel, a microbiologist 1024 and taxonomist who made significant contributions to the understanding of the physiology and 1025 applications of lactic acid bacteria). 1026 Strains of Holzapfelia are Gram positive, rod‐shaped, catalase negative, homofermentative, and 1027 aerotolerant. The type strain of the single species in the genus was isolated from mountain flowers, 1028 other strains were identified in bee larvae. H. floricola grows at 15 but not at 37°C; glucose and 1029 fructose are the only carbohydrates that are fermented. The sources of isolation as well as genomic 1030 and physiological properties of the organism indicate an insect‐ and flower associated lifestyle of the 1031 genus. 1032 The type species of Holzapfelia is H. floricola. 1033 Description of Holzapfelia floricola comb. nov. 1034 Holzapfelia floricola (flo.ri’co.la. L. fem. n. flos flower, blossom; L. suff. –cola from L. masc. or fem. n. 1035 incola dweller; N.L. fem. n. floricola flower‐dweller). 1036 Basonym: Lactobacillus floricola Kawasaki et al. 2011, 1358VP. 1037 The description of the species is identical of that of the genus (19). The genome size is 1.29 Mbp, the 1038 mol% GC content is 34.5. 1039 Isolated from flowers.

26

1040 The type strain is Ryu1‐2T = DSM 23037T = JCM 16512T = NRIC 0774T. 1041 Genome sequence accession number: AYZL00000000. 1042 16S rRNA gene accession number: AB523780.

1043 DESCRIPTION OF BOMBILACTOBACILLUS GEN. NOV. 1044 Bombilactobacillus (Bom.bi.lac.to.ba.cil’lus. L. masc. n. bombus, buzzing of bees and bumblebees, N.L. 1045 masc. n. Lactobacillus a bacterial genus; N.L. masc. n. Bombilactobacillus, a lactobacillus from bees 1046 and bumble bees. 1047 Bombilactobacillus species have been isolated from the stomach and the hindgut of honey bees (Apis 1048 mellifera) and bumble bees where they are associated with the heterofermentative sister genus 1049 Apilactobacillus. Bombilactobacillus species have genome sizes which range from 1.81 to 1.84 Mbp 1050 and a mol% GC content ranging from 34.7 to 39.5. They are homofermentative and thermophilic; 1051 comparable to other insect‐associated lactobacilli, bombilactobacilli ferment only a narrow spectrum 1052 of carbohydrates. 1053 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Bombilactobacillus is 1054 provided in Figure S6B. 1055 The type species is Bombilactobacillus mellifer comb. nov; Bombilactobacillus was previously referred 1056 to as L. mellifer group. 1057 Description of Bombilactobacillus mellifer comb. nov. 1058 Bombilactobacillus mellifer (mel’li.fer. L. masc. adj. mellifer, honey‐producing, referring to the origin 1059 from the stomach and digestive tract of honey bees Apis mellifera). 1060 Basonym: Lactobacillus mellifer Olofsson et al. 2014, 3113VP 1061 Description provided by [89]. B. mellifer grows over a wide temperature range (15 – 50°C) and pH 1062 values (pH 3 – 12) but ferments only few hexoses, sucrose, and raffinose [89]. The genome size is 1.82 1063 Mbp. The mol% GC content of DNA is 39.5. 1064 Isolated from isolated from the honey stomach of the honeybee Apis mellifera. 1065 The type strain is Bin4NT = DSM 26254T = CCUG 63291T. 1066 Genome sequence accession number: JXJQ00000000. 1067 16 rRNA gene sequence accession number: JX099543. 1068 Description of Bombilactobacillus bombi comb. nov. 1069 Bombilactobacillus bombi (bom’bi. L. masc. n. bombus, buzzing of bees and Bombus, N.L. gen. n. bombi 1070 of Bombus, of a bumblebee). 1071 Basonym: Lactobacillus bombi Killer et al. 2014, 2615VP 1072 Description provided by [113]; compared to other bombilactobacilli, B. bombi ferments a wider range 1073 of carbohydrates. 1074 The genome size is 1.84 Mbp. The mol% GC content of DNA is 34.7. 1075 Isolated from the digestive tract of laboratory‐reared bumblebee queens (Bombus terrestris). 1076 The type strain is BTLCH M1/2T = DSM 26517T = CCM 8440T.

27

1077 Genome sequence accession number: CP031513 (strain BI‐2.5; the genome sequence for the type 1078 strain is not available). 1079 16 rRNA gene sequence accession number: KJ078643. 1080 Description of Bombilactobacillus mellis comb. nov. 1081 Bombilactobacillus mellis (mel’lis. L. gen. n. mellis, of honey, referring to the isolation from the 1082 digestive tract of A. mellifera) 1083 Basonym: Lactobacillus mellis Olofsson et al. 2014, 3115VP 1084 The characteristics as provided by [89] are comparable to B. mellifer. The genome size is 1.81 Mbp. 1085 The mol% GC content of DNA is 36.4. 1086 Isolated from the honey stomach of the honeybee Apis mellifera. 1087 The type strain is Hon2NT = DSM 26255T = CCUG 63289T. 1088 Genome sequence accession number: JXBZ00000000. 1089 16 rRNA gene sequence accession number: JX099545. 1090 DESCRIPTION OF COMPANILACTOBACILLUS GEN. NOV 1091 Companilactobacillus (Com.pani.lac.to.ba.cil’lus. M. L. n. companio friend, partner; N.L. masc. n. 1092 Lactobacillus a bacterial genus; N.L. masc. n.; Companilactobacillus, Companion‐lactobacillus, the 1093 name refers to the association of Companilactobacillus species with other lactobacilli, particularly 1094 heterofermentative organisms, in cereal and vegetable fermentations [114]). 1095 Companilactobacillus spp. are Gram‐positive, homofermentative and non‐sporeforming rods. Strains 1096 of Companilactobacillus were isolated from fermented vegetables, particularly fermented mustard or 1097 onion greens, and fruits (17 type strains; 5 of these from mustard or onion fermentations), sourdough 1098 or related cereal fermentations (7 type strains), sausages or meat (7 type strains) or other plant 1099 sources; one isolates was obtained from a fermented dairy product. Companilactobacillus appears not 1100 to be dominant in any of these fermentations but occurs consistently (type I sourdoughs and 1101 fermented mustard or onion greens) or occasionally (meat, salami). Companilactobacillus 1102 metriopterae was isolated from a grasshopper and forms and outgroup that differs with respect to 1103 genome size (C. metriopterae 1.50 Mbp; other species range from 2.17 to 2.9 Mbp); mol% GC content 1104 of DNA (C. metriopterae 32.8; other species range from 34.1 to 38.6) and physiological properties. The 1105 temperature requirements for growth are inconsistent; all strains grow between 25 and 30°C, most 1106 but not all species grow at 15°C and some species grow at 45°C. The fermentation of pentoses by 1107 Companilactobacillus is species‐ or strain‐specific. Information on the ecology or lifestyle of 1108 companilactobacilli is scarce. 1109 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Companilactobacillus is 1110 provided in Figure S6C. 1111 The type species is Companilactobacillus alimentarius comb. nov; Companilactobacillus was previously 1112 referred to as L. alimentarius group. 1113 Description of Companilactobacillus alimentarius comb. nov. 1114 Companilactobacillus alimentarius (a.li.men.ta'ri.us. L. masc. adj. alimentarius related to food). 1115 Basonym: Lactobacillus alimentarius (ex Reuter 1970) Reuter 1983a, 672VP

28

1116 Growth is observed between 15 and 37°C and with pentoses, hexoses, and disaccharides as carbon 1117 source [115]. The genome size is 2.34 Mbp. The mol% GC content of DNA is 35.4. 1118 Isolated as spoilage organisms from marinated fish products, as fermentation organisms in fermented 1119 sausages, as spoilage organism in ready‐to‐eat meats. A strain of the species had been used as 1120 biopreservatives culture [116]. It occurs in association with Fructilactobacillus sanfranciscensis in type 1121 I sourdoughs [114] and was isolated in other plant fermentations. 1122 The type strain is R13T = ATCC 29643T= CCUG 30672T = CIP 102986T= DSM 20249T = JCM 1095T = LMG 1123 9187T. 1124 Genome sequence accession number: AZDQ00000000. 1125 16S RNA gene sequence accession number: M58804. 1126 Description of Companilactobacillus allii comb. nov. 1127 Companilactobacillus allii (al’li.i. L. gen. n. allii of Egyptian onions (Allium proliferum), the source of 1128 fermented onions, pa‐, from which the type strain was isolated). 1129 Basonym: Lactobacillus allii Jung et al. 2017, 4939VP 1130 Growth is observed at 25 and 37°C; hexoses and disaccharides but not pentoses are fermented [117]. 1131 The genome size is 2.51 Mbp. The mol% GC content of DNA is 35.3. 1132 Isolated from scallion kimchi. 1133 The type strain is WiKim39T=KCTC 21077T=JCM 31938T. 1134 Genome sequence accession numbers: CP019323 (chromosome) and CP019324 (). 1135 16S RNA gene sequence accession number: NR_159082. 1136 Description of Companilactobacillus baiquanensis comb. nov. 1137 Companilactobacillus baiquanensis (bai.quan.en´sis. N.L. masc. adj. baiquanensis, pertaining to 1138 Baiquan, a county in the Heilongjiang province of China). 1139 Basonym: Lactobacillus baiquanensis Wei and Gu 2019, 3192VP 1140 The type strain grows at 15 and 37 but not at 45°C; DL‐lactic acid is produced from ribose, hexoses, 1141 and maltose [118]. The genome size is 2.24 Mbp; the mol% G+C content is 34.4. 1142 Isolated from fermented from Chinese cabbage. 1143 The type strain is 184‐8T = LMG 31050T = NCIMB 15152T = CCM 8895T = KCTC 21131T. 1144 Genome sequence accession number: RHOQ00000000. 1145 16S RNA gene sequence accession number: MK110828. 1146 Description of Companilactobacillus bobalius comb. nov. 1147 Companilactobacillus bobalius (bo.ba’li.us. N.L. masc. adj. bobalius pertaining to the grape variety 1148 Bobal). 1149 Basonym: Lactobacillus bobalius Mañes‐Lázaro et al. 2008, 2702VP; the validity of the species was 1150 questioned but re‐established on the basis of ANI values [119]. 1151 Growth occurs in the range of 15 to 40°C and with pentoses, hexoses, and disaccharides as carbon 1152 sources [120]. The genome size is 2.88 Mbp. The mol% GC content of DNA is 35.3.

29

1153 Isolated from grape must and forage. 1154 The type strain is 203T = CECT 7310T = DSM 19674T = JCM 16180T. 1155 Genome sequence accession number: AZDY00000000. 1156 16S RNA gene sequence accession number: AY681134. 1157 Description of Companilactobacillus crustorum comb. nov. 1158 Companilactobacillus crustorum (crus.tor’um. L. gen. pl. n. crustorum, of baked goods or cakes). 1159 Basonym: Lactobacillus crustorum Scheirlinck et al. 2007, 1466VP 1160 Growth is observed at 15 and at 45°C; pentoses are not fermented; fermentation is strain 1161 dependent [121]. The genome size is 2.22 Mbp. The mol% GC content of DNA is 35. 1162 Isolated from sourdough, dairy products and forages. Some strains degrade saponins by β‐ 1163 glucuronidase activity [122]. 1164 The type strain is CCUG 53174T = JCM 15951T = LMG 23699T. 1165 Genome sequence accession number: AZDB00000000. 1166 16S RNA gene sequence accession number: AM285450. 1167 Description of Companilactobacillus farciminis comb. nov. 1168 Companilactobacillus farciminis (far.ci'mi.nis. L. gen. n. farciminis of sausage). 1169 Basonym: Lactobacillus farciminis Reuter 1983, 672VP 1170 Growth is observed between 15 and 42°C and with hexoses and disaccharides but not with pentoses 1171 as carbon source [115]. The genome size is 2.48 Mbp. The mol% GC content of DNA is 36.4. 1172 Isolated from meat products, sourdough, fermentend fish, cold‐smoked salmon, soy sauce mash, dairy 1173 products, table olives and fermented vegetables and corn silage. 1174 The type strain is Rv4 naT = ATCC 29644T= DSM 20184T = JCM 1097T= LMG 9200T = NRRL B‐4566T. 1175 Genome sequence accession number: AZDR00000000. 1176 16S RNA gene sequence accession number: M58817. 1177 Description of Companilactobacillus formosensis comb. nov. 1178 Companilactobacillus formosensis (for.mo.sen’sis. N.L. masc. adj. formosensis of or pertaining to 1179 Formosa [Taiwan] where the type strain was isolated). 1180 Basonym: Lactobacillus formosensis Chang et al. 2015, 105VP 1181 Growth is observed between 25 and 45°C but not at 10°C; hexoses and disaccharides are fermented; 1182 pentoses are not fermented [123]. The genome size is 2.47 Mbp. The mol% GC content of DNA is 35.5. 1183 Isolated from fermented soybean meal for use as poultry feed; it has been used experimentally as 1184 silage inoculant. 1185 The type strain is S215T=NBRC 109509T=BCRC 80582T. 1186 Genome sequence accession number: QWDI00000000. 1187 16S RNA gene sequence accession number: AB794060.

30

1188 Description of Companilactobacillus furfuricola comb. nov. 1189 Companilactobacillus furfuricola (fur.fu.ri’co.la. L. masc. n. furfur rice bran; L. suff. –cola from L. masc. 1190 or fem. n. incola inhabitant; N.L. masc. n. furfuricola rice bran‐inhabitant). 1191 Basonym: Lactobacillus furfuricola Irisawa et al. 2014, 2904VP 1192 Growth is observed between 20 and 37°C [124]. The genome size is 2.64 Mbp. The mol% GC content 1193 of DNA is 38.6. 1194 Isolated from rice bran paste for Japanese pickles. 1195 The type strain is Nu 27T=JCM 18764T=NRIC 0900T=DSM 27174T. 1196 Genome sequence accession number: RHNT00000000. 1197 16S RNA gene sequence accession number: AB910349. 1198 Description of Companilactobacillus futsaii comb. nov. 1199 Companilactobacillus futsaii (fut.sai’i. N.L. gen. n. of futsai, the Taiwanese fermented mustard product 1200 from which the type strain was isolated). 1201 Basonym: Lactobacillus futsaii Chao et al. 2012, 489VP. Two subspecies of C. futsaii, “C. futsaii ssp. 1202 futsaii” and “C. futsaii ssp. chongqingii” were described [125] but have not yet been included on the 1203 Validation Lists. The two subspecies are highly similar with respect to DNA‐DNA hybridization values, 1204 16rRNA and recA gene sequence similarity and were established on the basis of a divergent pheS 1205 sequence, requiring further confirmation. 1206 Growth is observed between 15 and 30°C; hexoses and disaccharides but not pentoses support acid 1207 formation [126]. The genome size is 2.53 Mbp. The mol% GC content of DNA is 35.6. 1208 Isolated from traditional fermented mustard products, fu‐tsai and suan‐tsai; it has been used 1209 experimentally for fermentation of shrimp waste [127]. 1210 The type strain is YM 0097T = BCRC 80278T = JCM 17355T. 1211 Genome sequence accession number: AZDO00000000 1212 16S RNA gene sequence accession number: HQ322270.S 1213 Description of Companilactobacillus ginsenosidimutans sp. nov. 1214 Companilactobacillus ginsenosidimutans (gin.se.no.si.di.mu’tans N.L. neut. n. ginsenosidium, 1215 ginsenoside, L. pres. part. mutans transforming, N.L. part. adj. ginsenosidimutans, ginsenoside 1216 converting). 1217 Effective publication Jung et al. 2013 as Lactobacillus ginsenosidimutans. C. ginsenosidimutans is a 1218 kimchi isolate that converts ginsenosides by β‐glucosidase activity [128]. The genome size is 2.59 Mbp. 1219 The mol% GC content of DNA is 36.7. 1220 Isolated from kimchi. 1221 The type strain is EMML 3041T = KACC 15420T = LMG 31607T = DSM 24154T. 1222 Genome sequence accession number: CP012034. 1223 16S RNA gene sequence accession number: HQ389549.

31

1224 Description of Companilactobacillus halodurans sp. nov. 1225 Companilactobacillus halodurans (ha.lo.du’rans. Gr. n. hals, halos salt; L. pres. part. durans enduring; 1226 N.L. part. adj. halodurans salt‐enduring, resisting). 1227 Effective publication Schuster et al., 2019, as Lactobacillus halodurans. C. halodurans grows between 1228 10 and 37°C and between pH 4.0 and 8.0, and at NaCl concentrations of up to 14% [129]. Acid is 1229 produced from ribose, hexoses, and some disaccharides. The genome size is 2.84 Mbp. The mol% GC 1230 content of DNA is 35.8. 1231 Isolated from spoiled fermented sausage. 1232 The type strain is TMW1.2172T = DSM 109452T = LMG31402T. 1233 Genome sequence accession number: VDFP00000000. 1234 16S RNA gene sequence accession number MK968448. 1235 Description of Companilactobacillus heilongjiangensis comb. nov. 1236 Companilactobacillus heilongjiangensis (hei.long.ji.ang.en’sis. N.L. masc. adj. heilongjiangensis 1237 pertaining to Heilongjiang, a river flowing through the province of China where the bacterium was 1238 isolated). 1239 Basonym: Lactobacillus heilongjiangensis Gu et al. 2013, 4098VP 1240 Hexoses and disaccharides but not pentoses are fermented [130]. The genome size is 2.79 Mbp. The 1241 mol% GC content of DNA is 37.5. 1242 Isolated from fermented vegetables and type I sourdough. 1243 The type strain is S4‐3T = LMG 26166T = DSM 28069T = NCIMB 14701T. 1244 Genome sequence accession number: CP012559. 1245 16S RNA gene sequence accession number: JF411966. 1246 Description of Companilactobacillus huachuanensis comb. nov. 1247 Companilactobacillus huachuanensis (hua.chuan.en´sis. N.L. masc. adj. huachuanensis pertaining to 1248 Huachuan County, a county in the Heilongjiang province of China). 1249 Basonym: Lactobacillus huachuanensis Fu and Gu 2019, 2812VP 1250 The physiological properties of C. huachuanensis are comparable to C. heilongjiangensis [131]. The 1251 genome size is 3.02 Mbp. The mol% GC content of DNA is 36.4. 1252 Isolated from fermented Chinese cabbage. 1253 The type strain is 395‐6.2T = CCM 8927T = NCIMB15188T = LMG31179T. 1254 Genome sequence accession number: BJDF00000000. 1255 16S RNA gene sequence accession number: LC438522. 1256 Description of Companilactobacillus hulinensis comb. nov. 1257 Companilactobacillus hulinensis (hu.lin.en´sis. N.L. masc. adj. hulinensis, pertaining to Hulin, a county 1258 in the Heilongjiang province of China). 1259 Basonym: Lactobacillus hulinensis Wei and Gu, 2019, 10VP

32

1260 Growth is observed at 15 and 37 but not at 45°C; DL‐lactic acid is produced from hexoses and pentoses 1261 [118]. The genome size is 2.35 Mbp, the mol% G+C is 36.7. 1262 Isolated from fermented Chinese cabbage. 1263 The type strain is 8‐1(1)T = LMG 31047T = NCIMB 15156T = CCM 8898T = KCTC 21115T. 1264 Genome sequence accession number: RHOO00000000. 1265 16S RNA gene sequence accession number: MK110830. 1266 Description of Companilactobacillus insicii comb. nov. 1267 Companilactobacillus insicii (in.si’ci.i. L. gen. n. insicii from minced meat). 1268 Basonym: Lactobacillus insicii Ehrmann et al. 2016, 241VP 1269 Growth is observed in the range of 8 – 45°C [132]; the genome size is 2.54 Mbp. The mol% GC content 1270 of DNA is 34.9. 1271 Isolated from pork salami. 1272 The type strain is TMW 1.2011T = CECT 8802T = DSM 29801T. 1273 Genome sequence accession number: RHNU00000000. 1274 16S RNA gene sequence accession number: KP677494. 1275 Description of Companilactobacillus jidongensis comb. nov. 1276 Companilactobacillus jidongensis (ji.dong.en´sis. N.L. masc. adj. jidongensis, pertaining to Jidong, a 1277 county in the Heilongjiang province of China). 1278 Basonym: Lactobacillus jidongensis Wei and Gu 2019, 3192VP 1279 Growth is observed at 10 but not at 37°C; DL‐lactic acid is produced from hexoses but not from 1280 pentoses [118]. The genome size is 2.71 Mbp. The mol% GC content of DNA is 36.5. 1281 Isolated from fermented Chinese cabbage. 1282 The type strain is 204‐8T = LMG31054T = NCIMB15159T = CCM8900T = KCTC21133T = LMG31054T. 1283 Genome sequence accession number: RHOP00000000. 1284 16S RNA gene sequence accession number: MK110829. 1285 Description of Companilactobacillus kedongensis comb. nov. 1286 Companilactobacillus kedongensis (ke.dong.en´sis. N.L. masc. adj. kedongensis, pertaining to Kedong, 1287 a county in the Heilongjiang province of China). 1288 Basonym: Lactobacillus kedongensis Wei and Gu 2019, 3191VP 1289 Characteristics of C. kedongensis are generally similar to C. jidongensis [118]. The genome size is 2.27 1290 Mbp, the mol% G+C content is 36.2. 1291 Isolated from fermented Chinese cabbage. 1292 The type strain is 116‐2T = LMG31051T = NCIMB 15158T = CCM 8899T = KCTC 21124T. 1293 Genome sequence accession number: RHOR00000000. 1294 16S RNA gene sequence accession number: MK110817.

33

1295 Description of Companilactobacillus keshanensis comb. nov. 1296 Companilactobacillus keshanensis (ke.shan.en´sis. N.L. masc. adj. keshanensis, pertaining to a county 1297 in the Heilongjiang province of China). 1298 Basonym: Lactobacillus keshanensis Wei and Gu 2019, 3191VP 1299 Characteristics of C. keshanensis are similar to C. jidongensis [118]. The genome size is 2.30 Mbp. The 1300 mol% GC content of DNA is 35.6. 1301 Isolated from fermented Chinese cabbage. 1302 The type strain is 33‐7T = LMG 31166T = NCIMB 15153T = CCM 8936T = KCTC 21118T = LMG 31166T. 1303 Genome sequence accession number: RHOS00000000. 1304 16S RNA gene sequence accession number: MK110816. 1305 Description of Companilactobacillus kimchiensis comb. nov. 1306 Companilactobacillus kimchiensis (kim.chi.en’sis. N.L. gen. n. kimchiensis from kimchi, a Korean 1307 fermented‐vegetable food). 1308 Basonym: Lactobacillus kimchiensis Kim et al. 2013, 1358VP. 1309 Hexoses and disaccharides but not pentoses are fermented; growth is observed at 15 – 37°C [133]. 1310 The genome size is 2.70 Mbp. The mol% GC content of DNA is 35.5. 1311 Isolated from kimchi. 1312 The type strain is L133T = DSM 24716T = JCM 17702T = KACC 15533T. 1313 Genome sequence accession number: JQCF00000000. 1314 16S RNA gene sequence accession number: HQ906500. 1315 Description of Companilactobacillus kimchii comb. nov. 1316 Companilactobacillus kimchii (kim’chi.i. N.L. gen. n. kimchii from kimchi, a Korean fermented‐ 1317 vegetable food). 1318 Basonym: Yoon et al. 2000, 1794VP; the classification of this taxon as a separate 1319 species has been questioned but was confirmed on the basis of ANI values [119]. 1320 Growth occurs in the range of 10 to 40°C and with pentoses, hexoses, and disaccharides as carbon 1321 sources [134]. The genome size is 2.74 Mbp. The mol% GC content of DNA is 35.1. 1322 Isolated from kimchi. 1323 The type strain is MT‐1077T = ATCC BAA‐131T = DSM 13961T = JCM 10707T = KCTC 8903PT. 1324 Genome sequence accession number: AZDH00000000. 1325 16S RNA gene sequence accession number: AF183558. 1326 Description of Companilactobacillus metriopterae comb. nov. 1327 Companilactobacillus metriopterae (me.tri.o.pte’rae. N.L. fem. gen. n. metriopterae of Metrioptera, 1328 the genus of grasshoppers from which the type strain was isolated). 1329 Basonym: Lactobacillus metriopterae Chiba et al. 2018, 1486VP; the species includes strains previously 1330 described as Lactobacillus terrae Kim et al. 2018 [135, 136]

34

1331 C. metriopterae forms an outgroup of Companilactobacillus and has the smallest genome size (1.50 1332 Mbp) and mol% GC content (32.8); it seems to transition to an insect associated lifestyle. C. 1333 metriopterae is pigmented and ferments fewer carbohydrates than other companilactobacilli. 1334 Isolated from the gut of grasshopper Metrioptera engelhardti, other isolates were obtained from soil. 1335 The type strain is Hime 5‐1T=JCM 31635T=DSM 103730T. 1336 Genome sequence accession number: RSTD00000000. 1337 16S RNA gene sequence accession number: LC190736. 1338 Description of Companilactobacillus mindensis comb. nov. 1339 Companilactobacillus mindensis (min.den’sis. N.L. adj. mindensis from Minden, Germany, where the 1340 type strain was isolated). 1341 Basonym: Lactobacillus mindensis Ehrmann et al. 2003, 11VP 1342 Growth is observed between 15 and 30°C. Pentoses are not fermented [137]. The genome size is 2.34 1343 Mbp. The mol% GC content of DNA is 38.2. 1344 Isolated from a type I sourdough. 1345 The type strain is TMW 1.80T = CCUG 48642T = DSM 14500T = JCM 12532T = LMG 21508T. 1346 Genome sequence accession number: AZEZ00000000. 1347 16S RNA gene sequence accession number: AJ313530. 1348 Description of Companilactobacillus mishanensis comb. nov. 1349 Companilactobacillus mishanensis (mi.shan.en´sis. N.L. masc. adj. mishanensis, pertaining to Mishan, 1350 a county in the Heilongjiang province of China). 1351 Basonym: Lactobacillus mishanensis Wei and Gu 2019, 3193VP 1352 Characteristics are similar to C. hulinensis [118]. The genome size is 2.47 Mbp, the mol% G+C is 36.6. 1353 Isolated fermented from Chinese cabbage. 1354 The type strain is 256‐3T = LMG 31048T = NCIMB 15160T = CCM 8901T = LMG 31048T. 1355 Genome sequence accession number: RHON00000000. 1356 16S RNA gene sequence accession number: MK110831. 1357 Description of Companilactobacillus musae comb. nov. 1358 Companilactobacillus musae (mu’sae. N.L. gen. n. musae of Musa; pertaining to banana fruit from 1359 Musa paradisiaca var. sapientum). 1360 Basonym: Lactobacillus musae Chen et al. 2017, 5148VP 1361 Growth is observed between 25 and 37°C and with hexoses and disaccharides but not with pentoses 1362 as carbon sources [138]. The genome size is 2.35 Mbp. The mol% GC content of DNA is 34.6. 1363 Isolated from banana fruits. 1364 The type strain is 313T=NBRC 112868T = BCRC 81020T. 1365 Genome sequence accession number: BIFW00000000. 1366 16S RNA gene sequence accession number: LC184607.

35

1367 Description of Companilactobacillus nantensis comb. nov. 1368 Companilactobacillus nantensis (nan.ten’sis. N.L. masc. adj. nantensis pertaining to Nantes, from 1369 where the first stain of this species was isolated). 1370 Basonym: Lactobacillus nantensis Valcheva et al. 2006, 589VP 1371 Growth occurs at 15 but not at 45°C; a wide range of carbohydrates including ribose, hexoses, and 1372 disaccharides are fermented [139]. The genome size is 2.91 Mbp. The mol% GC content of DNA 36.2. 1373 Isolated from a type I sourdough. 1374 The type strain is LP33T = TMW 1.1265T = CIP 108546T = DSM 16982T = JCM 16171T. 1375 Genome sequence accession number: AZFV00000000. 1376 16S RNA gene sequence accession number: AY690834. 1377 Description of Companilactobacillus nodensis comb. nov. 1378 Companilactobacillus nodensis (no.den’sis. N.L. masc. adj. nodensis referring to Noda, the Japanese 1379 city in which the type strain was isolated). 1380 Basonym: Lactobacillus nodensis Kashiwagi et al. 2009, 64VP 1381 Growth is observed between 15 and 37 °C and with pentoses and hexoses but not disaccharides as 1382 carbon source [140]. The genome size is 2.68 Mbp. The mol% GC content of DNA is 37.6. 1383 Isolated from fermented rice bran paste and has been used experimentally as adjunct culture in 1384 cheese [141]. 1385 The type strain is iz4b‐1T = DSM 19682T = JCM 14932T. 1386 Genome sequence accession number: AZDZ00000000. 1387 16S RNA gene sequence accession number: AB332024. 1388 Description of Companilactobacillus nuruki comb. nov. 1389 Companilactobacillus nuruki (nu.ru’ki. N.L. gen. n. nuruki of Nuruk, a Korean traditional rice 1390 ). 1391 Basonym: Lactobacillus nuruki Heo et al. 2018, 3277VP 1392 Growth is observed between 4 and 40°C; a wide spectrum of carbohydrates including pentoses, 1393 hexoses, and disaccharides is fermented [142]. 1394 The genome size is 2.58 Mbp. The mol% GC content of DNA is 34.2. 1395 Isolated from Nuruk, a rice bran fermentation starter. 1396 The type strain is SYF10‐1aT = KACC 18726T = NBRC 112011T. 1397 Genome sequence accession number: NIPR00000000. 1398 16S RNA gene sequence accession number: MG786754. 1399 Description of Companilactobacillus paralimentarius comb. nov. 1400 Companilactobacillus paralimentarius (par.a.li.men.ta’ri.us. Gr. pref. para beside; L. masc. adj. 1401 alimentarius, a species epithet; N.L. masc. adj. paralimentarius beside C. alimentarius, referring to the 1402 close relationship with this organism). 1403 Basonym: Lactobacillus paralimentarius Cai et al. 1999, 1455VP

36

1404 The physiological properties of C. paralimentarius as described [143] are similar to C. alimentarius. 1405 The genome size is 2.55 Mbp. The mol% GC content of DNA is 35.1. 1406 Isolated from sourdough, other cereal fermentations, and from poultry meat. 1407 The type strain is TB 1T = CCUG 43349T = CIP 106794T = DSM 13238T = JCM 10415T = LMG 19152T. 1408 Genome sequence accession number: AZES00000000. 1409 16S RNA gene sequence accession number: AB018528. 1410 Description of Companilactobacillus salsicarnum sp. nov. 1411 Companilactobacillus salsicarnum (sal.si.carn´um. L. adj. salsus, salted; L. gen.n. carnis of meat; N.L. 1412 gen. n. salsicarnum of salted meat, referring to salami as the source of isolation). 1413 Effective publication Schuster et al., 2019 as Lactobacillus salsicarnum. C. salsicarnum grows between 1414 10 and 37°C and between pH 4.5 and 8.5, and at NaCl concentrations of up to 8% [129]. Acid is 1415 produced from ribose and arabinose, hexoses, and maltose and trehalose. The genome size is 2.43 1416 Mbp. The mol% GC content of DNA is 36.6. 1417 Isolated from spoiled fermented sausage. 1418 The type strain is TMW 1.2098T = DSM 109451T = LMG 31401T. 1419 Genome sequence accession number: VDFN00000000. 1420 16S RNA gene sequence accession number MK968446. 1421 Description of Companilactobacillus suantsaicola comb. nov. 1422 Companilactobacillus suantsaicola (suan.tsai'co.la. N.L. neut. n. suantsaium, from suan‐tsai, 1423 fermented mustard greens; L. suff. –cola from L. masc. or fem. n. incola inhabitant; N.L. masc. n. 1424 suantsaicola occurring in suan‐tsai.) 1425 Basonym: Lactobacillus suantsaicola Lin et al. 2019, 8VP 1426 Growth is observed between 20 and 37°C and at pH 4.0 to 10.0 [144]. The genome size is 2.60 Mbp. 1427 The mol% GC content of DNA is 36.9. 1428 Isolated from suan‐tsai, a traditional fermented mustard green product of Taiwan. 1429 The type strain is R7T = BCRC 81127T = NBRC 113530T. 1430 Genome sequence accession number: RKLY00000000. 1431 16S RNA gene sequence accession number: MH810311. 1432 Description of Companilactobacillus tucceti comb. nov. 1433 Companilactobacillus tucceti (tuc.ce’ti. L. gen. n. tucceti, from a sausage, referring to the origin of the 1434 type strain). 1435 Basonym: Lactobacillus tucceti Chenoll et al. 2009, 925VL 1436 The type strain grows at 15 and 37 but not at 45°C [145]. The genome size is 2.17 Mbp. The mol% GC 1437 content of DNA is 34.1. 1438 Isolated from sausage. 1439 The type strain is R 19cT = CECT 5920T = DSM 20183T = JCM 18037T. 1440 Genome sequence accession number: AZDG00000000.

37

1441 16S RNA gene sequence accession number: AJ576006. 1442 Description of Companilactobacillus versmoldensis comb. nov. 1443 Companilactobacillus versmoldensis (vers.mold.en’sis. N.L. masc. adj. versmoldensis is pertaining to 1444 Versmold, the town in Germany where the strains were isolated). 1445 Basonym: Lactobacillus versmoldensis Kröckel et al. 2003, 516VP 1446 Description is provided by [146]. The genome size is 2.37 Mbp. The mol% GC content of DNA is 38.3. 1447 Isolated from poultry salami. 1448 The type strain is KU‐3T = ATCC BAA‐478T = DSM 14857T = JCM 16174T = NCCB 100034T. 1449 Genome sequence accession number: AZFA00000000. 1450 16S RNA gene sequence accession number: AJ496791. 1451 Description of Companilactobacillus zhachilii comb. nov. 1452 Companilactobacillus zhachilii (zha.chi’li.i. N.L. gen. n. zhachilii of zha‐chili, a Chinese fermented 1453 mustard green product). 1454 Basonym: Lactobacillus zhachilii Zhang et al., 2019, 2199VP 1455 Growth is observed between 15 and 45°C and with a wide range of hexoses and disaccharides but not 1456 with pentoses [147]. The genome size is 2.71 Mbp. The mol% GC content of DNA is 36.3. 1457 Isolated from Zha‐Chili, a traditional fermented product from mustard greens. 1458 The type strain is HBUAS52074T = GDMCC1.1417T = KCTC21106T. 1459 Genome sequence accession number: CP031933. 1460 16S RNA gene sequence accession number: MH392835. 1461 Description of Companilactobacillus zhongbaensis comb. nov. 1462 Companilactobacillus zhongbaensis (zhong.ba.en´sis. N.L. masc. adj. zhongbaensis from Zhongba, a 1463 county in Tibet, China, where the type strain was isolated). 1464 Basonym: Lactobacillus zhongbaensis Wei and Gu 2019, 3193VP 1465 Growth is observed at 15 and 37 but not at 45°C; DL‐lactic acid is produced from a broad range of 1466 pentoses, hexoses, and disaccharides [118]. The genome size is 3.04 Mbp, the mol% G+C is 39.4. 1467 Isolated from a fermented dairy product. 1468 The type strain is M1575T = LMG 31045T = NCIMB 15149T = CCM 8892T. 1469 Genome sequence accession number: RHOM00000000. 1470 16S RNA gene sequence accession number: MK110832. 1471 DESCRIPTION OF LAPIDILACTOBACILLUS GEN. NOV. 1472 Lapidilactobacillus (La.pi.di.lac.to.ba.cil’lus L. masc. n. lapis, stone, referring to the isolation source of 1473 the type species Lapidilactobacillus concavus; N.L. masc. n. Lactobacillus a bacterial genus; N.L. masc. 1474 n. Lapidilactobacillus, a lactobacillus isolated from stone [walls]). 1475 The cells are Gram‐positive rods or cocci, homofermentative, non motile, non‐spore‐forming, 1476 facultatively anaerobes, and catalase‐negative. The pH‐range for growth and pentose utilization is

38

1477 strain dependent, the optimum pH is between 6.0 and 7.0. They are homofermentative and mainly 1478 produce L‐lactic acid. The optimum temperature for growth is 30–37 °C. No ammonia is produced from 1479 . The mol% GC content of DNA is between 38.1 and 49.0. 1480 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Lapidiactobacillus is 1481 provided in Figure S6D. 1482 The type species is Lapidilactobacillus concavus comb. nov.; Lapidilactobacillus was previously 1483 referred to as L. concavus / dextrinicus group. 1484 Description of Lapidilactobacillus concavus comb. nov. 1485 Lapidilactobacillus concavus (con.ca’vus. L. masc. adj. concavus, curved, referring to the curved shape 1486 of the cells). 1487 Basonym: Lactobacillus concavus Tong and Dong 2005, 2201VP 1488 Cells of L. concavus are non‐motile curved rods; the optimum pH for growth is 6.0‐6.4; they can also 1489 grow at 8% (v/v) ethanol but not in 6.5% (w/v) NaCl [148]. The genome size of the type strain is 1.90 1490 Mbp. The mol% GC content of DNA is 43.3. 1491 Isolated from the walls of a distilled‐spirit‐fermenting cellar in China. 1492 The type strain is C‐5‐1T = DSM 17758T = AS 1.5017T = JCM 14153T = LMG 22739T. 1493 Genome sequence accession number: AZFX00000000. 1494 16S rRNA gene accession number: AY683322. 1495 Description of Lapidilactobacillus bayanensis comb. nov. 1496 Lapidilactobacillus bayanensis (ba.yan.en´sis. N.L. masc. adj. bayanensis pertaining to Bayan, a county 1497 in the Heilongjiang province of China). 1498 Basonym: Lactobacillus bayanensis Wei and Gu 2019, 3191VP 1499 Cells grow at 15 but not at 37°C. L(+)‐lactic acid and D(‐)‐lactic acid are produced from glucose, 1500 fructose, mannose, and maltose; pentoses or other disaccharides are not fermented [118]. The 1501 genome size of the type strain is 2.43 Mbp. The mol% GC content of DNA is 40.1. 1502 Isolated from fermented Chinese cabbage. 1503 The type strain 54‐5T = LMG 31166T = NCIMB 15153T = CCM 8936T = KCTC 21118T. 1504 Genome sequence accession number: RHOX00000000. 1505 16S rRNA gene accession number: MK110807. 1506 Description of Lapidilactobacillus dextrinicus comb. nov. 1507 Lapidilactobacillus dextrinicus (dex.tri′ni.cus. N.L. neut. n. dextrinum, dextrin; L. suff. ‐icus, suffix used 1508 with the sense of belonging to; N.L. masc. adj. dextrinicus, related to dextrin). 1509 Basonym: Lactobacillus dextrinicus (Coster and White 1964) Haakensen et al. 2009, 620VP. 1510 Strains of L. dextrinicus were previously classified as Pediococcus dextrinicus (Coster and White 1964) 1511 Back 1978 (Approved Lists 1980) or Pediococcus cerevisiae subsp. dextrinicus. Cells are spherical, and 1512 may occur singly, in pairs or clusters and rarely in chains. Clusters of four may be observed, but they 1513 do not divide in two perpendicular directions at right angles. Only L(+)‐lactic acid is produced from 1514 maltose, dextrin and starch [149]. The genome size of the type strain is 1.81 Mbp. The mol% GC 1515 content of DNA is 38.1.

39

1516 Isolated from silage, fermenting vegetables, beer and sliced vacuum‐packed cooked sausage. 1517 The type strain is ATCC 33087T = CCUG 18834T = CIP 103407T = DSM 20335T = JCM 5887T = LMG 11485T 1518 = NCIMB 701561T = VKM B‐1603T. 1519 Genome sequence accession number: AYYK00000000. 1520 16S rRNA gene accession number: D87679. 1521 DESCRIPTION OF AGRILACTOBACILLUS GEN. NOV. 1522 Agrilactobacillus (A.gri.lac.to.ba.cil’lus. L. adj.masc. n. ager, a field; N.L. masc. n. Lactobacillus, a 1523 bacterial genus; Agrilactobacillus, a lactobacillus from fields or soil). 1524 Gram positive, rod‐shaped, catalase negative, homofermentative, and aerotolerant. The genome size 1525 ranges from 2.33 to 3.47 Mbp; the mol% GC content of DNA ranges from 42.1 ‐ 44.0. Origin, 1526 physiological properties and genome characteristics suggest a free‐living lifestyle of the genus. 1527 Isolated from compost that included shochu mash, and from vegetables (mustard) in Indonesia and 1528 China. 1529 The type species of the genus is A. composti. 1530 Description of Agrilactobacillus composti comb. nov. 1531 Agrilactobacillus composti (com.pos’ti. N.L. gen. n. composti of compost, the source of the type strain). 1532 Basonym: Lactobacillus composti Endo and Okada 2007, 872VP 1533 The type strain grows over a relatively wide pH range and in the range of 10 to 37°C but not at 45°C 1534 [150]. The genome size is 3.47 Mbp and the mol% GC content of DNA is 44.0. 1535 Isolated from compost from shochu mash solids and from pulque, a Mexican alcoholic beverage [151]. 1536 The type strain is NRIC 0689T = DSM 18527T = JCM 14202T. 1537 Genome sequence accession number: AZGA00000000. 1538 16S rRNA gene accession number: AB268118. 1539 Description of Agrilactobacillus yilanensis comb. nov. 1540 Agrilactobacillus yilanensis (yi.lan.en´sis. N.L. masc. adj. yilanensis pertaining to Yilan, a county in the 1541 Heilongjiang province of China). 1542 Basonym: Lactobacillus yilanensis Wei and Gu 2019, 3189VP 1543 The type strain grows at 15 but not at 45°C and ferments a wide range of pentoses, hexoses, and 1544 disaccharides [118]. The genome size is 2.33 Mbp and the mol% GC content of DNA is 41.7. 1545 Isolated from a Chinese cabbage fermentation. 1546 The type strain is 54‐2T = LMG 31058T = NCIMB 15154T=CCM 8896T=KCTC 21120T. 1547 Genome sequence accession number: RHOY00000000. 1548 16S rRNA gene accession number: MK110806. 1549 DESCRIPTION OF SCHLEIFERILACTOBACILLUS GEN. NOV. 1550 Schleiferilactobacillus (Schlei.fer.i.lac.to.ba.cil’lus. L. masc. noun Schleiferi, of (Karl‐Heinz) Schleifer, a 1551 German microbiologist and taxonomist who made seminal contributions to bacterial taxonomy.

40

1552 N.L.masc. n. Lactobacillus a bacterial genus; N.L. masc. n. Schleiferilactobacillus, a lactobacillus named 1553 after Karl‐Heinz Schleifer). 1554 Gram positive, rod‐shaped, catalase negative, homofermentative, and aerotolerant. Strain of the 1555 genus were isolated from spoiled beverages including beer and fermented dairy beverages, fermented 1556 vegetables, and fermented cereals. Growth is observed in the range of 15 – 42°C; a wide range of 1557 carbohydrates including pentoses, hexoses and oligosaccharides are fermented. The genome size 1558 ranges from 3.14 ‐ 3.32 Mbp; the mol% GC content of DNA ranges from 49.1 to 56.3. 1559 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Schleiferilactobacillus is 1560 provided in Figure S6E. 1561 The type species of the genus is S. perolens comb. nov.; Schleiferilactobacillus was previously referred 1562 to as L. perolens group. 1563 Description of Schleiferilactobacillus perolens comb. nov. 1564 Schleiferilactobacillus perolens (per.o'lens, Latin preposition per through, penetrating; L. pres. part. 1565 olens having an odor; N.L. part. adj. perolens smelling, referring to the copious diacetyl production by 1566 strains of the species). 1567 Basonym: Lactobacillus perolens Back et al. 2000, 3VP 1568 Description of the species is as provided by [152]. Spoilage was attributed to copious amounts of 1569 diacetyl produced by S. perolens. The genome size is 3.31 Mbp and the mol% GC content of DNA is 1570 49.1. 1571 Isolated from spoiled soft drinks and brewery environments. 1572 The type strain is L 533T = DSM 12744T = JCM 12534T = LMG 18936T. 1573 Genome sequence accession number: AZEC00000000. 1574 16S rRNA gene accession number: Y19167. 1575 Description of Schleiferilactobacillus harbinensis comb. nov. 1576 Schleiferilactobacillus harbinensis (har.bi.nen’sis. N.L. masc. adj. harbinensis pertaining to Harbin, a 1577 city in northeastern China where the type strain was isolated). 1578 Basonym: Lactobacillus harbinensis Miyamoto et al. 2006, 2VL 1579 Description of the species is as provided by [153]. The genome size is 3.14 Mbp and the mol% GC 1580 content of DNA is 53.8. 1581 Isolated from fermented vegetables “Suan Cai”, the brewery environment, fermented cereals and 1582 tomato pomace, and spoiled soft drinks. 1583 The type strain is AHU 1762T = DSM 16991T = JCM 16178T = NBRC 100982T = SBT 10908T. 1584 Genome sequence accession number: AZFW00000000. 1585 16S rRNA gene accession number: AB196123. 1586 Description of Schleiferilactobacillus shenzhenensis comb. nov. 1587 Schleiferilactobacillus shenzhenensis (shen.zhen.en’sis. N.L. masc. adj. shenzhenensis of Shenzhen, the 1588 city in the South of China where the type strain was isolated). 1589 Basonym: Lactobacillus shenzhenensis Zou et al. 2013, 1821VP

41

1590 Growth is observed at 15 and 45 °C [154]. The genome size is 3.27 Mbp and the mol% GC content of 1591 DNA is 56.3. 1592 Isolated from a fermented dairy beverage. 1593 The type strain is LY‐73T = CCTCC M 2011481T = KACC 16878T. 1594 Genome sequence accession number: AVAA00000000. 1595 16S rRNA gene accession number: JX523627. 1596 DESCRIPTION OF LACTICASEIBACILLUS GEN. NOV. 1597 Lacticaseibacillus (Lac.ti.ca.se.i.ba.cil'lus. L. neut. n. lac milk; L. n. caseus cheese, referring to the casei‐ 1598 group lactobacilli; L. masc. n. bacillus a rod; N.L. masc. n. Lacticaseibacillus a milk derived rodlet from 1599 the [Lactobacillus] casei group). 1600 Strains of Lacticaseibacillus are homofermentative; some but not all species metabolize pentoses via 1601 the phosphoketolase pathway. The mol % GC content of DNA is between 46 and 58.0. The genome 1602 size ranges from 1.93 to 3.14 Mbp. Strains are non‐motile, oxidase negative, often producing D(‐)‐ and 1603 L(+)‐lactic acid from glucose. The temperature range for growth is variable, but never below 10°C and 1604 never above 45°C. One subspecies survives 70°C for 40 seconds. Lys‐D‐Asp is the most common type 1605 of the peptidoglycan. The genus has considerable economic importance as it harbors several species 1606 that are used as starter cultures in dairy fermentations and as probiotics [58, 59]. 1607 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Lacticaseibacillus is 1608 provided in Figure S6F. 1609 The type species is Lacticaseibacillus casei comb. nov.; Lacticaseibacillus was previously referred to as 1610 L. casei group. 1611 Description of Lacticaseibacillus casei comb. nov. 1612 Lacticaseibacillus casei (ca’se.i. L. gen. n. casei of cheese). 1613 Basonym: (Orla Jensen 1916, Hansen and Lessel 1971, 71 (Approved Lists) 1614 (Streptobacterium casei Orla‐Jensen 1919, 166). 1615 The species includes strains previously classified as Lactobacillus zeae [155]. Original characteristics of 1616 L. casei strains are provided by [2, 156, 157]. L. casei is differentiated from most other lactobacilli by 1617 catalase activity [47]. The genome size of the type strain is 2.83 Mbp. The mol% GC content of DNA is 1618 46.5. 1619 Isolates were obtained from diverse sources including chinese traditional pickle, infant feces, corn 1620 liquor, oat silage, commercial dietery supplements sputum, nasopharynx [47]. Information on the 1621 lifestyle of L. casei is counded by the unclear taxonomy over the past decades; most genomes of 1622 designated as L. casei in the NCBI database should be classified as L. paracasei instead [10, 47]. 1623 The type strain is 03 [7, IAM 12473, Orland L‐323, R.P. Tittsler 303]T = ATCC 393T = BCRC 10697T = 1624 CCUG 21451T = CECT 475T = CIP 103137T = DSM 20011T = IAM 12473T = NBRC 15883T = JCM 1134T = 1625 KCTC 3109T = LMG 6904T = NCIMB 11970T = NCIMB 11970T = NRRL B‐1922T. 1626 Genome sequence accession number: BALS00000000. 1627 16S rRNA gene accession number: AF469172.

42

1628 Description of Lacticaseibacillus baoqingensis comb. nov. 1629 Lacticaseibacillus baoqingensis (boa.qing.en’sis. N.L. masc. adj. boaqingensis of Boaqing, from where 1630 the type strain was isolated). 1631 Basonym: Lactobacillus baoqingensis Long and Gu 2019, 2347VP 1632 Original characteristics of L. baoqingensis strains are as provided by Long and Gu [158]. 1633 The genome size of the type strain is 2.86 Mbp. The mol% GC content of DNA is 50.9. 1634 Isolated from a vegetable fermentation. 1635 The type strain is 47‐3T = NCIMB 15165T = CCM 8903T = LMG 31064T. 1636 Genome sequence accession number: RHOI00000000. 1637 16S rRNA gene accession number: MK110840. 1638 Description of Lacticaseibacillus brantae comb. nov. 1639 Lacticaseibacillus brantae (bran′tae. N.L. gen. n. brantae, of Branta, isolated from Branta canadensis, 1640 Canada goose). 1641 Basonym: Lactobacillus brantae Volokhov et al. 2012, 2068VP 1642 Original characteristics of L. brantae strains are provided by [159]. The genome size of the type strain 1643 is 1.93 Mbp. The mol% GC content of DNA is 47.5. 1644 Isolated from the faeces of wild Canada goose (Branta canadensis) and from experimental 1645 sourdoughs. 1646 The type strain is SL1108T = ATCC BAA‐2142T = DSM 23927T = LMG 26001T. 1647 Genome sequence accession number: AYZQ00000000. 1648 16S rRNA gene accession number: HQ022861. 1649 Description of Lacticaseibacillus camelliae comb. nov. 1650 Lacticaseibacillus camelliae (ca.mel′li.ae. N.L. gen. n. camelliae, of Camellia sinensis fermented tea 1651 leaves). 1652 Basonym: Lactobacillus camelliae Tanasupawat et al. 2007, 1371VL [160] 1653 Original characteristics of L. camelliae strains are as provided by [161] .The genome size of the type 1654 strain is 2.57 Mbp. The mol% GC content of DNA is 55.4. 1655 Isolated from fermented tea (Camellia sinensis) leaves and fermented tomato pomace. 1656 The type strain is MCH3‐1T = BCC 21233T = DSM 22697T = JCM 13995T = NRIC 0672T. 1657 Genome sequence accession number: AYZJ00000000. 1658 16S rRNA gene accession number: AB257864. 1659 Description of Lacticaseibacillus chiayiensis comb. nov. 1660 Lacticaseibacillus chiayiensis (chia.yi.en’sis. N.L. masc. adj. chiayiensis of Chiayi, from where the type 1661 strain was isolated). 1662 Basonym: Lactobacillus chiayiensis effective publication Huang et al. 2018, 3382 (Approved Lists)

43

1663 Original characteristics of L. chiayiensis strains are provided by [162, 163]. The genome size of the type 1664 strain is 2.87 Mbp. The mol% GC content of DNA is 47.1. 1665 Isolated from cow manure. 1666 The type strain is NCYUAST = BCRC 81062T = NBRC 112906T. 1667 Genome sequence accession number: MSSM00000000. 1668 16S rRNA gene accession number: MF446960. 1669 Description of Lacticaseibacillus hulanensis comb. nov. 1670 Lacticaseibacillus hulanensis (hu.lan.en’sis. N.L. masc. adj. hulanensis pertaining to Hulan, a district of 1671 Harbin city in China). 1672 Basonym: Lactobacillus hulanensis Zhao and Gu et al. 2019, 5VP 1673 Original characteristics of L. hulanensis strains are provided [164]. The genome size of the type strain 1674 is 2.36 Mbp. The mol% GC content of DNA is 52.7. 1675 Isolated from suancai, fermented Chinese cabbage 1676 The type strain is ZW163T = NCIMB15193T = CCM8926T = CCTCC AB 2019015T. 1677 Genome sequence accession number: RRYD00000000. 1678 16S rRNA gene accession number: LC436604. 1679 Description of Lacticaseibacillus jixianensis comb. nov. 1680 Lacticaseibacillus jixianensis (ji.xian.en’sis. N.L. masc. adj. jixianensis pertaining to Jixian, a county in 1681 the Heilongjiang province of China). 1682 Basonym: Lactobacillus jixianensis Long and Gu, 2019, 2346VP 1683 Original characteristics of L. jixianensis strains are provided by [158]. The genome size of the type 1684 strain is 2.47 Mbp. The mol% GC content of DNA is 58.3. 1685 Isolated from fermented Chinese cabbage. 1686 The type strain is 159‐4T = CCM 8911 T = NCIMB 15175 T. 1687 Genome sequence accession number: RHOJ00000000. 1688 16S rRNA gene accession number: MK110836. 1689 Description of Lacticaseibacillus manihotivorans comb. nov. 1690 Lacticaseibacillus manihotivorans (ma.ni.ho.ti.vo’rans. N.L. neut. n. manihotum cassava; L. v. vorare 1691 to devour; N.L. part. adj. manihotivorans cassava‐devouring). 1692 Basonym: Lactobacillus manihotivorans Morlon‐Guyot et al. 1998, 1107VP 1693 Strains of L. manihotivorans express extracellular [165]. The genome size of the type strain 1694 is 3.14 Mbp. The mol% GC content of DNA is 47.7. 1695 Isolated from sour cassava starch fermentation and from tomato pomace silage. 1696 The type strain is OND 32T = CCUG 42894T = CIP 105851T = DSM 13343T = JCM 12514T = LMG 18010T. 1697 Genome sequence accession number: AZEU00000000. 1698 16S rRNA gene accession number: AF000162.

44

1699 Description of Lacticaseibacillus nasuensis comb. nov. 1700 Lacticaseibacillus nasuensis (na.su.en′sis. N.L. masc. adj. nasuensis, named after Nasu‐shiobara City, 1701 where strains were first isolated). 1702 Basonym: Lactobacillus nasuensis Cai et al. 2012, 1143VP 1703 Original characteristics of L. nasuensis strains are provided [166]. The genome size of the type strain 1704 is 2.28 Mbp. The mol% GC content of DNA is 57.0. 1705 Isolated from a Sudan grass [Sorghum sudanense (Piper) Stapf.] silage. 1706 The type strain is SU 18T = JCM 17158T = CGMCC 1.10801T. 1707 Genome sequence accession number: AZDJ00000000. 1708 16S rRNA gene accession number: AB608051. 1709 Description of Lacticaseibacillus pantheris comb. nov. 1710 Lacticaseibacillus pantheris (pan’ther.is. N.L. gen. n. pantheris of the panther, referring to the isolation 1711 of the strains from jaguar feces). 1712 Basonym: Lactobacillus pantheris Liu and Dong 2002, 1747VP 1713 Characteristics of the species are described in [167]. L. pantheris together with L. thailandensis, L. 1714 sharpie, L. songhuajiangensis and L. hulanensis forms a monophyletic outgroup to Lacticaseibacillus; 1715 however, physiological characteristics and their ecology, as far as data are available, are similar to 1716 other Lacticaseibacillus spp. The genome size of the type strain is 2.55 Mbp. The mol% GC content of 1717 DNA is 52.9. 1718 Isolated from the faeces of a jaguar in Beijing Zoo and from fermented vegetables. 1719 The type strain is A24‐2‐1T = DSM 15945T = AS 1.2826T = JCM 12539T = LMG 21017T. 1720 Genome sequence accession number: AZFJ00000000. 1721 16S rRNA gene accession number: AF413523. 1722 Description of Lacticaseibacillus paracasei comb. nov. 1723 Lacticaseibacillus paracasei (pa.ra.ca’se.i. Gr. prep. para resembling; N.L. gen. n. casei a species 1724 epithet; N.L. gen. n. paracasei resembling Lactobacillus casei). 1725 Basonym: Collins et al. 1989, 107VP 1726 Strains of this species including strains previously referred to as L. casei subsp. alactosus, L. casei 1727 subsp. pseudoplantarum and L. casei subsp. tolerans were transferred from L. casei [168]. Original 1728 characteristics of L. paracasei strains are described in [168]. Cells have superoxide dismutase activity 1729 [47], are rods (0.8–1.0 × 2.0–4.0 μm), often with square ends, occurring singly or in chains. Growth is 1730 observed between 10 and 40°C. Some strains grow at 5 and 45°C. Two subspecies are validly 1731 published. The genome size of the type strain is 2.88 Mbp. The mol% GC content of DNA is 46.5. 1732 Strains of this species have a nomadic lifestyle and were isolated from a variety of courses including 1733 the human oral cavity [169], fermented cereals, vegetables, meats, dairy products, and in invertebrate 1734 hosts. 1735 The type strain is DSM 5622T = ATCC 25302T = AS 1.2826T = JCM 8130T = LMG 13087T. 1736 Genome sequence accession number: AZGH00000000.

45

1737 16S rRNA gene accession number of the type strain: D79212. 1738 Two subspecies are recognized: Lacticaseibacillus paracasei subsp. paracasei and Lacticaseibacillus 1739 paracasei subsp. tolerans. 1740 Description of Lacticaseibacillus paracasei subsp. paracasei comb. nov. 1741 Lacticaseibacillus paracasei subsp. paracasei (pa.ra.ca’se.i. Gr. prep. para resembling; N.L. gen. n. 1742 casei a species epithet; N.L. gen. n. paracasei resembling Lactobacillus casei). 1743 Basonym Lactobacillus paracasei subsp. paracasei Collins et al. 1989, 107VP 1744 The genome size of the type strain is 2.88 Mbp. The mol% GC content of DNA is 46.5. 1745 Isolated from dairy products, sewage, silage, humans and clinical sources. 1746 The type strain is DSM 5622T = ATCC 25302T = AS 1.2826T = JCM 8130T T = LMG 13087T. 1747 Genome sequence accession number: AZGH00000000. 1748 16S rRNA gene accession number: D79212. 1749 Description of Lacticaseibacillus paracasei subsp. tolerans comb. nov. 1750 Lacticaseibacillus paracasei subsp. tolerans (to.le’rans. L. masc. part. tolerans tolerating, enduring; 1751 means survival during the pasteurization of milk). 1752 Basonym Lactobacillus paracasei subsp. tolerans Abo‐Elnaga and Kandler 1965, Collins et al. 1989, 1753 108VP 1754 Some strains of the subspecies were initially described as L. casei subsp. tolerans [168]. Original 1755 characteristics of L. paracasei subsp. tolerans strains are described in [170]. The genome size of the 1756 type strain is 2.38 Mbp. The mol% GC content of DNA is 46.4. 1757 Isolated from dairy products and tomato pomace silage. 1758 The type strain is 7/74T = ATCC 25599T = CCUG 34829T = CIP 102994T = CIP 103024T = DSM 20258T = 1759 NBRC 15906T = JCM 1171T = LMG 9191T = NCIMB 9709 T. 1760 Genome sequence accession number: AYYJ00000000. 1761 16S rRNA gene accession number of the type strain: AB181950. 1762 Description of Lacticaseibacillus porcinae comb. nov. 1763 Lacticaseibacillus porcinae (por.ci’nae. L. gen. n. porcinae of pork). 1764 Basonym Lactobacillus porcinae Nguyen et al. 2013, 1758VP 1765 Original characteristics of L. porcinae strains are described in [171]. The genome size of the type strain 1766 is 2.84 Mbp. The mol% GC content of DNA is 47.2. 1767 Isolate from nem chua (fermented beef) in northern Vietnam. 1768 The type strain is R‐42633T = CCUG 62266T = LMG 26767T. 1769 Genome sequence accession number: RHNS00000000. 1770 16S rRNA gene accession number: HE616585. 1771 Description of Lacticaseibacillus rhamnosus comb. nov. 1772 Lacticaseibacillus rhamnosus (rham.no’sus. N.L. masc. adj. rhamnosus pertaining to rhamnose).

46

1773 Basonym (Hansen 1968, Collins et al. 1989, 108VP (Lactobacillus casei subsp. 1774 rhamnosus Hansen 1968, 76.) 1775 Original characteristics of L. rhamnosus strains are described in by [172]. The genome size of the type 1776 strain is 2.95 Mbp. The mol% GC content of DNA is 46.7. 1777 The species has a nomadic lifestyle and was isolated from a broad range of habitats including dairy 1778 products, fermented meat, fish, vegetables and cereals, sewage, humans (oral, vaginal and intestinal), 1779 invertebrate hosts and clinical sources [17, 169]. 1780 The type strain is ATCC 7469T = CCUG 21452T = CIP A157T = DSM 20021T = NBRC 3425T = JCM 1136T = 1781 LMG 6400T = NCAIM B.01147T = NCCB 46033T = NCIMB 6375T = NCTC 12953T = NRRL B‐442T = VKM B‐ 1782 574T. 1783 Genome sequence accession number: AZCQ00000000. 1784 16S rRNA gene accession number: D16552. 1785 Description of Lacticaseibacillus saniviri comb. nov. 1786 Lactobacillus saniviri (sa.ni.vi′ri. L. masc. adj. sanus healthy; L. gen. n. viri, of a man; N.L. gen. n. saniviri, 1787 of a healthy man). 1788 Basonym Lactobacillus saniviri Oki et al. 2012, 605VP 1789 Original characteristics of L. saniviri strains are described in [173]. The genome size of the type strain 1790 is 2.44 Mbp. The mol% GC content of DNA is 47.7. 1791 Isolated from the faeces of a healthy man and from fermented rice and fish. 1792 The type strain is YIT 12363 T = JCM 17471 T = DSM 24301T. 1793 Genome sequence accession number: JQCE00000000. 1794 16S rRNA gene accession number: AB602569. 1795 Description of Lacticaseibacillus sharpeae comb. nov. 1796 Lacticaseibacillus sharpeae (shar’pe.ae. N.L. gen. n. sharpeae of Sharpe; named for M. Elisabeth 1797 Sharpe, an English bacteriologist). 1798 Basonym Lactobacillus sharpeae Weiss et al. 1981, 266VP 1799 Original characteristics of L. sharpeae strains are described in [174, 175]. The genome size of the type 1800 strain is 2.45 Mbp. The mol% GC content of DNA is 53.4. 1801 Isolated from municipal sewage and spoiled meat. 1802 The type strain is 71T = ATCC 49974T = CIP 101266T = DSM 20505T = JCM 1186T = LMG 9214T = NRRL B‐ 1803 14855T. 1804 Genome sequence accession number: AYYO00000000. 1805 16S rRNA gene accession number: M58831. 1806 Description of Lacticaseibacillus songhuajiangensis comb. nov. 1807 Lacticaseibacillus songhuajiangensis (song.hua.ji.ang.en’sis. N.L. masc. adj. songhuajiangensis 1808 pertaining to the Songhuajiang River, a river flowing through Heilongjiang Province of China). 1809 Basonym Lactobacillus songhuajiangensis Gu et al. 2013, 4698VP.

47

1810 Original characteristics of L. songhuajiangensis strains are described in [176]. The genome size of the 1811 type strain is 2.61 Mbp. The mol% GC content of DNA is 52.7. 1812 Isolated from traditional sourdough. 1813 The type strain is 7‐19T = LMG 27191T = NCIMB 14832T = CCUG 62990T. 1814 Genome sequence accession number: RHNR00000000. 1815 16S rRNA gene accession number: HF679038. 1816 Description of Lacticaseibacillus thailandensis comb. nov. 1817 Lacticaseibacillus thailandensis (thai.lan.den’sis. N.L. masc. adj. thailandensis, pertaining to Thailand, 1818 where the type strain was isolated). 1819 Basonym Lactobacillus thailandensis Tanasupawat et al. 2007, 1371VL 1820 Original characteristics of L. thailandensis strains are described in [161]. The genome size of the type 1821 strain is 2.06 Mbp. The mol% GC content of DNA is 53.5. 1822 Isolated from fermented fish (pla‐ra) in Thailand. 1823 The type strain is MCH5‐2T = BCC 21235T = DSM 22698T = JCM 13996T = NRIC 0671T. 1824 Genome sequence accession number: AYZK00000000. 1825 16S rRNA gene accession number: AB257863. 1826 EMENDED DESCRIPTION OF PARALACTOBACILLUS 1827 Paralactobacillus (Pa.ra.lac.to.ba.cil’lus. Gr. prep. para resembling; N.L. masc. n. Lactobacillus a 1828 bacterial genus; Paralactobacillus resembling the genus Lactobacillus). 1829 Cell are Gram‐positive, homofermentative, non‐motile, non‐spore‐forming rods, usually occurring 1830 singly or as pairs. They produce both D(‐)‐ and L(+)‐ lactic acid from glucose. They produce acid from 1831 mannose and salicin but not from lactose, melibiose, raffinose, ribose or xylose. They grow at 15°C 1832 but not at 45°C and with 6.5 % NaCl. 1833 The type species P. selangorensis was isolated from a Malaysian food ingredient, chili bo [177] and 1834 later transferred to the genus Lactobacillus, proposing Lactobacillus selangorensis comb. nov. [178]. 1835 Given the data presented in the present study we adopt the proposal of Leisner et al. [177]. 1836 Description of Paralactobacillus selangorensis comb. nov. 1837 Paralactobacillus selangoresis (se.lan.gor.en’sis. N.L. masc. adj. selangorensis, belonging to the 1838 province of Selangor, Malaysia); Leisner et al. 2000, Haakensen et al. 2011, 2982VP 1839 Cells are able to grow on acetate agar and can lower the pH to below 4.15 in La‐broth [179]. No growth 1840 occurs with 6.5% NaCl [177]. The genome size of the type strain is 2.09 Mbp; the mol % GC content of 1841 DNA is 46. 1842 The species was isolated from a Malaysian food ingredient called chili bo. 1843 The type strain is ATCC BAA‐66T = CCUG 43347T = CIP 106482T = DSM 13344T = LMG 17710T. 1844 Genome sequence accession number: JQAZ00000000. 1845 16S rRNA gene accession number: AF049745.

1846 DESCRIPTION OF LATILACTOBACILLUS GEN. NOV.

48

1847 Latilactobacillus (La.ti.lac.to.ba.cil'lus. L. masc. adj. latus wide, broad; N.L. masc. n. Lactobacillus a 1848 bacterial genus name; N.L. masc. n. Latilactobacillus a widespread lactobacillus). 1849 Species of Latilactobacillus are homofermentative, their mol% GC content is between 40 and 42 and 1850 the genome size ranges from 1.82 to 2.12 Mbp; they produce both D(–)‐ and L‐(+)‐lactic acid with the 1851 exception of L. fuchuensis, which produces only the L(+)‐ isomer. Strains in the species lead a free‐ 1852 living lifestyle and are mesophilic; many strains are psychrotrophic and grow below 8°C. L. sakei and 1853 L. curvatus have commercial importance as meat starter cultures [58, 59]. 1854 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Latilactobacillus is 1855 provided in Figure S6G. 1856 The type species is Latilactobacillus sakei comb. nov.; Latilactobacillus was previously referred to as L. 1857 sakei group. 1858 Description of Latilactobacillus sakei comb. nov. 1859 Latilactobacillus sakei (sa’ke.i. N.L. gen. n. sakei of sake). 1860 Basonym: corrig. Katagiri, Kitahara and Fukami 1934, 157 (Approved Lists); emend. 1861 Klein et al. 1996 1862 L. sakei strains are frequently slightly curved and irregular cells, especially during stationary growth 1863 phase. Many of the strains grow also at 2–4°C, the majority of them produce L(+)‐lactic acid in MRS 1864 broth [180]. 1865 Isolated from sauerkraut, fermented plant material, fermented seafood, cold smoked salmon, 1866 fermented or refrigerated meat products, spontaneous sourdoughs, and prepacked finished dough 1867 [181]. It is used commercially as starter culture for fermented meats [58, 59]. 1868 Two subspecies are recognised: Latilactobacillus sakei subsp. carnosus and Latilactobacillus sakei 1869 subsp. sakei. 1870 Description of Latilactobacillus sakei subsp. carnosus comb. nov. 1871 Latilactobacillus sakei subsp. carnosus (car.no’sus. L. masc. adj. carnosus pertaining to meat). 1872 Basonym: Lactobacillus sakei subsp. carnosus Torriani et al. 1996, 1162VP 1873 L. sakei subsp. carnosus was formerly also referred to as Lactobacillus curvatus subsp. melibiosus 1874 [182]. Characteristics of the species are described in [183]. The genome size of the type strain is 1.99 1875 Mbp. The mol% GC content of DNA is 41.0. 1876 Isolated from fermented meat products, vacuum‐packaged meat, sauerkraut, and other fermented 1877 plant material. 1878 The type strain is R 14b/aT = LMG 17302T = DSM 15831T = CCUG 31331T = CIP 105422T = JCM 11031T. 1879 Genome sequence accession number: AZFG00000000. 1880 16S rRNA gene accession number: AY204892. 1881 Description of Latilactobacillus sakei subsp. sakei comb. nov. 1882 Latilactobacillus sakei subsp. sakei (sa’ke.i. N.L. gen. n. sakei of sake). 1883 Basonym: Lactobacillus sakei subsp. sakei corrig. Katagiri, Kitahara and Fukami 1934, 157 (Approved 1884 Lists); emend. Klein et al., 1996

49

1885 L. sakei subsp. sakei strains produce ammonia from arginine and acetoin from glucose and they grow 1886 in the presence of 10% NaCl. The genome size of the type strain is 1.91 Mbp. The mol% GC content of 1887 DNA is 41.1. 1888 Isolated from sake starter, fermented meat products, vacuum‐packaged meat, sauerkraut and other 1889 fermented plant material, and human faeces [183]. 1890 The type strain is T.S [K. Kitahara 37]T = ATCC 15521T= LMG 9468T = DSM 20017T = CCUG 30501T = CIP 1891 103139T = IFO (now NBRC) 15893T = JCM 1157T. 1892 Genome sequence accession number: AZDN00000000. 1893 16S rRNA gene accession number: AM113784. 1894 Description of Latilactobacillus curvatus comb. nov. 1895 Latilactobacillus curvatus (cur.va′tus. L. masc. adj. curvatus curved). 1896 Basonym: Lactobacillus curvatus (Bacterium curvatum Troili‐Petersson 1903, 137) Abo‐Elnaga and 1897 Kandler 1965; Troili‐Petersson 1980 (Approved Lists); emend. Klein et al. 1996 1898 Some L. curvatus strains are motile [184]; they occur in pairs, short chains, and frequently in horseshoe 1899 forms. Characteristics of the species are provided by [170, 180, 185]. The genome size of the type 1900 strain is 1.82 Mbp. The mol% GC content of DNA is 42.0. 1901 Isolated from cow dung, fermented and vacuum‐packaged refrigerated meat and fish products, dairy 1902 products such as milk and cheese, fermented plant products like sauerkraut, sourdough (including 1903 prepacked finished dough and pressed ), radish, pickles and kimchi, other plant‐derived materials 1904 like honey and from the environmental fermentation process of corn or grass silage [186]. 1905 The type strain is 1T = LMG 9198T = DSM 20019T = LMG 13553T = ATCC 25601T= CCUG 30669T = CIP 1906 102992T = IFO (now NBRC) 15884T = JCM 1096T = NRRL B‐4562T. 1907 Genome sequence accession number: AZDL00000000. 1908 16S rRNA gene accession number: AM113777. 1909 Description of Latilactobacillus fuchuensis comb. nov. 1910 Latilactobacillus fuchuensis (fu.chu.en’sis. N.L. masc. adj. fuchuensis of Fuchu, the city where this 1911 bacterium was originally isolated). 1912 Basonym: Lactobacillus fuchuensis Sakala et al. 2002, 1153VP 1913 Original characteristics of L. fuchuensis strains are described in [187]. The genome size of the type 1914 strain is 2.12 Mbp. The mol% GC content of DNA is 41.8. 1915 Isolated from vacuum‐packaged refrigerated beef, common carp intestine and other seafood 1916 products. 1917 The type strain is B5M10T = DSM 14340T = CCUG 47133T = JCM 11249T. 1918 Genome sequence accession number: AZEX00000000. 1919 16S rRNA gene accession number: AB370875. 1920 Description of Latilactobacillus graminis comb. nov. 1921 Latilactobacillus graminis (gra’mi.nis. L. gen. n. graminis of grass). 1922 Basonym: Lactobacillus graminis Beck et al. 1989, 93VP (Effective publication: Beck et al. 1988, 282)

50

1923 Strains of this species show a flocculant sediment after three days of growth in MRS broth [188]. The 1924 genome size of the type strain is 1.84 Mbp. The mol% GC content of DNA is 40.3. 1925 Isolated from grass silage, meat products, sourdough, gut of snail Cornum aspersum and grapes. 1926 The type strain is G90(1)T = LMG 9825T = DSM 20719T = ATCC 51150T= CCUG 32238T = CIP 105164T = 1927 JCM 9503T = NRRL B‐14857T. 1928 Genome sequence accession number: AYZB00000000. 1929 16S rRNA gene accession number: AM113778. 1930 DESCRIPTION OF LOIGOLACTOBACILLUS GEN. NOV. 1931 Loigolactobacillus (Loi.go.lac.to.ba.cil’lus. Gr. masc. n. loigos destruction, ruin, havoc; N.L. masc. n 1932 Lactobacillus a bacterial genus; Loigolactobacillus, a lactobacillus with spoilage potential). 1933 Cells are are non‐motile, non‐spore‐forming, Gram‐positive, catalase negative rods, found singly and 1934 in pairs. They are homofermentative and produce both D‐(−)‐ and L‐(+)‐ lactic acid isomers. Pentose 1935 fermentation is species specific; most of species produce acid from D‐mannose and D‐mannitol. The 1936 mol% GC content is between 40.6 and 44.3. 1937 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Loigolactobacillus is 1938 provided in Figure S6H. 1939 The type species of the genus is L. coryniformis comb. nov.; Loigolactobacillus was previously referred 1940 to as L. coryniformis group. 1941 Description of Loigolactobacillus coryniformis comb. nov. 1942 Loigolactobacillus coryniformis (co.ry.ni.for′mis. Gr. fem. n. coryne a club; L. fem. n. forma shape; N.L. 1943 masc. adj. coryniformis club‐shaped). 1944 Basonym: Lactobacillus coryniformis Abo‐Elnaga and Kandler 1965, 18 (Approved Lists) 1945 L. coryniformis cells are short, coccoid rods, frequently pear‐shaped. Pantothenic acid, niacin, 1946 riboflavin, biotin, and p‐aminobenzoic acid are essential for the growth of all or the majority of the 1947 strains tested [170]. 1948 Two subspecies are recognized: Loigolactobacillus coryniformis subsp. coryniformis and 1949 Loigolactobacillus coryniformis subsp. torquens. 1950 Description of Loigolactobacillus coryniformis subsp. coryniformis comb. nov. 1951 Loigolactobacillus coryniformis subsp. coryniformis (co.ry′ni.for′mis. Gr. n. coryne a club; L. adj. formis 1952 shaped; N.L. adj. coryniformis club‐shaped). 1953 Basonym: Lactobacillus coryniformis subsp. coryniformis Abo‐Elnaga and Kandler 1965, 18 (Approved 1954 Lists) 1955 L. coryniformis subsp. coryniformis strains produce L‐(+) isomer of the lactis acid at amounts of 15‐ 1956 20% of total lactic acid [170]. The genome size of the type strain is 2.71 Mbp. The mol% GC content of 1957 DNA is 42.9. 1958 Isolated from silage, cow dung, dairy barn air and sewage, and from table olives, wheat, pickled 1959 vegetable, cheese and ting, a fermented sorghum porridge. 1960 The type strain is ATCC 25602T = CIP 103133T = DSM 20001T = CCUG 30666T = JCM 1164T = LMG 9196T 1961 = NRRL B‐4391T.

51

1962 Genome sequence accession number: AZCN00000000. 1963 16S rRNA gene accession number: M58813. 1964 Description of Loigolactobacillus coryniformis subsp. torquens comb. nov. 1965 Loigolactobacillus coryniformis subsp. torquens (tor’quens. L. part. adj. torquens, twisting). 1966 Basonym: Lactobacillus coryniformis subsp. torquens Abo‐Elnaga and Kandler 1965, 18 (Approved 1967 Lists) 1968 L. coryniformis subsp. torquens strains exclusively produce D(‐)‐lactic acid [170]. The genome size of 1969 the type strain is 2.78 Mbp. The mol% GC content of DNA is 42.9. 1970 Isolated from cheese, yaks’ milk cheese, silage and tomato pomace silage. 1971 The type strain is CECT 4129 = ATCC 25600T = CCUG 30667T = CIP 103134T = DSM 20004T = JCM 1166T 1972 = LMG 9197T = NRRL B‐4390T. 1973 Genome sequence accession number: AZDC00000000. 1974 16S rRNA gene accession number: AJ575741. 1975 Description of Loigolactobacillus backii comb. nov. 1976 Loigolactobacillus backii (back′i.i. N.L. gen. n. backii, named in recognition of Werner Back, a German 1977 microbiologist who contributed to the microbiological and technological development of brewing). 1978 Basonym: Lactobacillus backii Tohno et al. 2013, 3858VP 1979 L. backii strains are rod‐shaped and occur singly, in pairs and in chains; they show leucin 1980 aminopeptidase, valine aminopeptidase, cystine aminopeptidase, acid phosphatase, naphthol‐AS‐BI‐ 1981 phosphohydrolase, β‐galactosidase, β ‐glucosidase and N‐acetyl‐ β ‐glucosaminidase activities [189]. 1982 The genome size of the type strain is 2.78 Mbp. The mol% GC content of DNA is 40.7. 1983 Isolated from a spoiled lager beer. 1984 The type strain is L‐1062 = JCM 18665T = LMG 23555T = DSM 18080T = L1062T. 1985 Genome sequence accession number: ASM166367v1. For bioinformatics analysis, the closed genome 1986 of strain TMW1.1989 was used: CP014873 (chromosome), CP014874 (plasmid) and CP014875 (second 1987 plasmid). 1988 16S rRNA gene accession number: AB779648. 1989 Description of Loigolactobacillus bifermentans comb. nov. 1990 Loigolactobacillus bifermentans (bi.fer.men′tans. L. pref. bi twice; L. pres. part. fermentans leavening; 1991 N.L. part. adj. bifermentans doubly fermenting). 1992 Basonym: Lactobacillus bifermentans (ex Pette and van Beynum 1943) Kandler et al. 1983, 896VP 1993 L. bifermentans strains are non‐motile irregular rods with rounded or often tapered ends; clumps are 1994 often observed. Lactic acid is fermented to acetic acid, ethanol, traces of propionic acid, carbon

1995 dioxide and free H2 [190]. The genome size of the type strain is 3.14 Mbp. The mol% GC content of 1996 DNA is 44.3. 1997 Isolated from spoiled Edam and Gouda cheeses where it forms undesired small cracks [191], from 1998 fermented masau fruits and from Himalayan fermented milk products.

52

1999 The type strain is N2T = ATCC 35409T = CCUG 32234T = CIP 102811T = DSM 20003T = JCM 1094T = LMG 2000 9845T. 2001 Genome sequence accession number: AZDA00000000. 2002 16S rRNA gene accession number: JN175330. 2003 Description of Loigolactobacillus iwatensis comb. nov. 2004 Loigolactobacillus iwatensis (i.wa.ten’sis. N.L. masc. adj. iwatensis of or belonging to Mount Iwate, 2005 where the first strains were isolated). 2006 Basonym: Lactobacillus iwatensis Tohno et al. 2013, 3856VP 2007 L. iwatensis strains are facultatively anaerobic, non‐spore‐forming and non‐motile rods. They are 2008 homofermentative; they are positive for C4 esterase, leucine aminopeptidase, valine aminopeptidase 2009 and acid phosphatase [189]. The genome size of the type strain is 2.62 Mbp. The mol% GC content of 2010 DNA is 40.6. 2011 Isolated from orchardgrass silage. 2012 The type strain is IWT246T = JCM 18838T = DSM 26942T. 2013 Genome sequence accession number: RHNP00000000. 2014 16S rRNA gene accession number: AB773428. 2015 Description of Loigolactobacillus jiayinensis comb. nov. 2016 Loigolactobacillus jiayinensis (jia.yin.en’sis. N.L. masc. adj. jiayinensis, pertaining to Jiayin, a county in 2017 the Heilongjiang province of China). 2018 Basonym: Lactobacillus jiayinensis Long and Gu 2019, 2348VP 2019 Cells are non‐motile, rod‐shaped, singly or in pairs [158]. The genome size of the type strain is 3.04 2020 Mbp. The mol% GC content of DNA is 42.6. 2021 Isolated from a fermentation Chinese cabbage. 2022 The type strain is 257‐1T = NCIMB 15166T = CCM 8904T = LMG 31065T. 2023 Genome sequence accession number: RHOF00000000. 2024 16S rRNA gene accession number: MK110846. 2025 Description of Loigolactobacillus rennini comb. nov. 2026 Loigolactobacillus rennini (ren.ni’ni. N.L. gen. n. rennini, of rennet). 2027 Basonym: Lactobacillus rennini Chenoll et al. 2006, 451VP 2028 L. rennini strains are non‐motile rods, found singly and in pairs. They grow at pH 3.7, 4.5 and 8.0, and 2029 in medium with 5 and 10% (w/v) NaCl [192]. The genome size of the type strain is 2.27 Mbp. The mol% 2030 GC content of DNA is 40.7. 2031 Isolated from rennet and are associated with cheese spoilage. 2032 The type strain is 1‐7T = CECT 5922T = DSM 20253T = JCM 14279T. 2033 Genome sequence accession number: AYYI00000000. 2034 16S rRNA gene accession number: LC258150.

53

2035 Description of Loigolactobacillus zhaoyuanensis comb. nov. 2036 Loigolactobacillus zhaoyuanensis (zhao.yuan.en’sis. N.L. masc. adj. zhaoyuanensis, pertaining to 2037 Zhaoyuan, a county in the Heilongjiang province of China). 2038 Basonym: Lactobacillus zhaoyuanensis Long and Gu, 2019, 2348VP 2039 Cells are non‐motile rods, usually singly or in pairs. They grow at 15–33°C and pH 5–10. Both isomers 2040 of lactic acid are produced (93 % D(‐)‐lactate and 7 % L(+)‐lactate) [158]. The genome size of the type 2041 strain is 2.70 Mbp. The mol% GC content of DNA is 42.7. 2042 Isolated from fermented Chinese cabbage. 2043 The type strain is 187‐3T = NCIMB 15172T = CCM 8910T. 2044 Genome sequence accession number: RHOE00000000. 2045 16S rRNA gene accession number: MK110851. 2046 DESCRIPTION OF DELLAGLIOA GEN. NOV. 2047 Dellaglioa (Del.la.gli.o’a. N.L. fem. n. Dellaglioa, named after Franco Dellaglio, an Italian 2048 microbiologist, former chairman of the Subcommittee on taxonomy of Bifidobacterium, Lactobacillus 2049 and related organisms, known for his significant research contributions to the taxonomy of the lactic 2050 acid bacteria). 2051 Strains of Dellaglioa are facultatively anaerobic, psychrophilic, nonmotile, homofermentative rod‐ 2052 shaped bacteria. Strains of the only species included in the genus are psychrotrophic and occur as 2053 meat spoilage organism. 2054 The type species is Dellaglioa algida. 2055 Description of Dellaglioa algida comb. nov. 2056 Dellaglioa algida (al’gi.da. L. fem. adj. algida cold, referring to the ability to grow at low temperature). 2057 Basonym: Lactobacillus algidus Kato et al. 2000, 1148VP 2058 Characteristics are described in [193]. The genome size of the type strain is 1,59 Mbp, the mol % GC 2059 content of DNA is 36. 2060 Isolated as spoilage organisms from refrigerated beef and pork meat. 2061 The type strain is M6A9T = JCM 10491T = LMG 19872T = DSM 15638T = CIP 106688T. 2062 Genome sequence accession number: AZDI00000000. 2063 16S rRNA gene accession number: AB033209. 2064 DESCRIPTION OF LIQUORILACTOBACILLUS GEN. NOV. 2065 Liquorilactobacillus (Li.quo.ri.lac.to.ba.cil’lus L. masc. n. liquor, liquid; N.L. masc. n. Lactobacillus a 2066 bacterial genus; N.L. masc. n. Liquorilactobacillus a lactobacillus from liquids, referring to the isolation 2067 of most species from liquids including , plant sap, and alcoholic beverages). 2068 Homofermentative, their mol% GC content is between 33.9 and 40.0; most of the species are motile 2069 with the exception of L. cacaonum, L. hordei, L. mali. They contain meso‐diaminopimelic acid. 2070 Liquorilactobacillus species were mostly isolated from fermented plant materials including alcoholic 2071 fermentations and water kefir. Many strains of Liquorilactobacillus produce dextran from sucrose 2072 [194].

54

2073 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Liquorilactobacillus is 2074 provided in Figure S6I. 2075 The type species is Liquorilactobacillus mali comb. nov.; Liquorilactobacillus species were previously 2076 considered part of the L. salivarius group. 2077 Description of Liquorilactobacillus mali comb. nov. 2078 Liquorilactobacillus mali (ma’li. L. gen. n. mali, of an apple). 2079 Basonym: Lactobacillus mali Carr and Davies 1970, 769 (Approved Lists); emend. Kaneuchi et al. 1988, 2080 272 2081 L. mali cells are non‐motile or weakly motile with a few peritrichous flagella. Liquid cultures are turbid 2082 after few days, with subsequent clearing and sediment. They produce acetoin and dextran; malic acid

2083 is decomposed to lactic acid and CO2. Most strains have a pseudocatalase activity when they grow on 2084 MRS agai with 0.1 % (w/v) glucose [195, 196]. The genome size of the type strain is 2.59. The mol% GC 2085 content of DNA is 36.1. 2086 Isolated from wine must, fermenting cider, fermented molasses, water , cocoa bean 2087 fermentations and table olives. 2088 The type strain is ATCC 27053T = CCUG 30141T = CCUG 32228T = CIP 103142T = DSM 20444T = JCM 2089 1116T = LMG 6899T = NBRC 102159T = NCIB (now NCIMB) 10560T = NRRL B‐4563T = VKM B‐1600T. 2090 Genome sequence accession number: AYYH00000000. 2091 16S rRNA gene accession number: M58824. 2092 Description of Liquorilactobacillus aquaticus comb. nov. 2093 Liquorilactobacillus aquaticus (a.qua′ti.cus. L. masc. adj. aquaticus, living, growing or found in water, 2094 or an aquatic environment). 2095 Basonym: Lactobacillus aquaticus Mañes‐Lázaro et al. 2009, 2217VP 2096 L. aquaticus cells are motile rods, which grow at pH 4.5‐8.0 but not at pH 3.3. There is no growth in 5 2097 or 10% NaCl. 2098 The species is described in [197]. The genome size of the type strain is 2.41 Mbp. The mol% GC content 2099 of DNA is 37.4. 2100 Isolated from a eutrophic freshwater pond. 2101 The type strain is IMCC1736T = CECT 7355T = DSM 21051T = JCM 16869T. 2102 Genome sequence accession number: AYZD00000000. 2103 16S rRNA gene accession number: DQ664203. 2104 Description of Liquorilactobacillus cacaonum comb. nov. 2105 Liquorilactobacillus cacaonum (ca.ca.o′num. N.L. gen. pl. n. cacaonum, of cacao beans). 2106 Basonym: Lactobacillus cacaonum De Bruyne et al. 2009, 11VP 2107 L. cacaonum cells are non‐motile small rods, they grow at 37C in MRS broth at pH 3.9; no growth is 2108 observed in MRS supplemented with NaCl [198]. The genome size of the type strain is 1.92 Mbp. The 2109 mol% GC content of DNA is 33.9. 2110 Isolated from cocoa fermentation. 2111 The type strain is R‐34119T = DSM 21116T = LMG 24285T.

55

2112 Genome sequence accession number: AYZE00000000. 2113 16S rRNA gene accession number: AM905389. 2114 Description of Liquorilactobacillus capillatus comb. nov. 2115 Liquorilactobacillus capillatus (ca.pil.la’tus. L. masc. adj. capillatus, hairy, referring to the characteristic 2116 of having long, hairy flagella). 2117 Basonym: Lactobacillus capillatus Chao et al. 2008, 2557VP 2118 L. capillatus cells are motile by means of peritrichous flagella; they grow at pH 4.0 and pH 8.0 but they 2119 do not grow at 8% NaCl [199]. The genome size of the type strain is 2.24 Mbp. The mol% GC content 2120 of DNA is 37.6. 2121 Isolated from fermented brine used for stinky tofu production. 2122 The type strain is YIT 11306T = BCRC 17811T = DSM 19910T = JCM 15044T. 2123 Genome sequence accession number: AZEF00000000. 2124 16S rRNA gene accession number: AB365976. 2125 Description of Liquorilactobacillus ghanensis comb. nov. 2126 Liquorilactobacillus ghanensis (gha.nen′sis. N.L. masc. adj. ghanensis, pertaining to Ghana, where the 2127 species was first isolated). 2128 Basonym: Lactobacillus ghanensis Nielsen et al. 2007, 1471VP 2129 L. ghanensis cells are motile with peritrichous flagella, and colonies have slightly uneven edges after 2130 3‐4 days of anaerobic growth. They do not grow at pH 8.0, nor at 6.5% NaCl [200]. The genome size of 2131 the type strain is 2.61 Mbp. The mol% GC content of DNA is 37.1. 2132 Isolated from cocoa fermentations. 2133 The type strain is L489T = CCUG 53453T = DSM 18630T = JCM 15611T. 2134 Genome sequence accession number: AZGB00000000. 2135 16S rRNA gene accession number: DQ523489. 2136 Description of Liquorilactobacillus hordei comb. nov. 2137 Liquorilactobacillus hordei (hor’de.i. L. gen. n. hordei, from barley). 2138 Basonym: Lactobacillus hordei Rouse et al. 2008, 2016VP 2139 L. hordei cells are non‐motile rods, they grow at pH 4 and 8 but not at pH 3 and 9. They produce 2140 [201]. The genome size of the type strain is 2.30 Mbp. The mol% GC content of DNA is 2141 34.8. 2142 Isolated from malted barley, water kefirs and in Turkish traditional fermented gilaburu fruit juice. 2143 The type strain is UCC128T = DSM 19519T = JCM 16179T = LMG 24241T. 2144 Genome sequence accession number: AZDX00000000. 2145 16S rRNA gene accession number: EU074850. 2146 Description of Liquorilactobacillus nagelii comb. nov. 2147 Lacitilactobacillus nagelii (na.gel’i.i. N.L. gen. n. nagelii, of Nagel, after Charles W. Nagel, Washington 2148 State University, USA, for his contributions to the science of wines).

56

2149 Basonym: Lactobacillus nagelii Edwards et al. 2000, 700VP 2150 L. nagelii cells are motile rods, they grow in MRS broth with 5%(w/v) NaCl (pH 4.5) at 25°C; both citrate 2151 and malate are utilized in the presence of glucose and dextran is formed from sucrose [202]. The 2152 genome size of the type strain is 2.50 Mbp. The mol% GC content of DNA is 36.7. 2153 Isolated from partially fermented wine, spontaneous cocoa bean fermentations, water kefirs, 2154 fermented cassava food and silage fermentation of fruit residues.

T T T T T 2155 The type strain is LuE10 = ATCC 700692 = CCUG 43575 = DSM 13675 = JCM 12492 . 2156 Genome sequence accession number: AZEV00000000. 2157 16S rRNA gene accession number: Y17500. 2158 Description of Liquorilactobacillus oeni comb. nov. 2159 Liquorilactobacillus oeni (oe′ni. Gr. masc. n. oinos, wine; N.L. gen. n. oeni, of wine). 2160 Basonym: Lactobacillus oeni Mañes‐Lázaro et al. 2009, 2013VP 2161 L. oeni cells are mostly motile and they grow at pH 4.5‐8.0 but not at pH 3.3 and with 10% ethanol. L‐ 2162 Malic acid is transformed into L(+)‐lactic acid. They produce exopolysaccharide from sucrose [203]. 2163 The genome size of the type strain is 2.12 Mbp. The mol% GC content of DNA is 37.3. 2164 Isolated from Bobal wine. 2165 The type strain is 59bT = CECT 7334T = DSM 19972T = JCM 18036T. 2166 Genome sequence accession number: AZEH00000000. 2167 16S rRNA gene accession number: AY681127. 2168 Description of Liquorilactobacillus satsumensis comb. nov. 2169 Liquorilactobacillus satsumensis (sat.su.men′sis. N.L. masc. adj. satsumensis, pertaining to Satsuma, 2170 old name for the southern part of Kyushu in Japan, from where the type strain was isolated). 2171 Basonym: Lactobacillus satsumensis Endo and Okada 2005, 85VP 2172 L. satsumensis cells are motile rods with peritrichous flagella. Growth is observed in MRS broth at pH 2173 3.5 containing 5% (w/v) NaCl but not with 10% (v/v) ethanol. Dextran is formed from sucrose [204]. 2174 The genome size of the type strain is 2.65 Mbp. The mol% GC content of DNA is 39.9. 2175 Isolated from mashes of shochu, a traditional Japanese distilled spirit made from fermented rice and 2176 other starchy materials. 2177 The type strain is DSM 16230T = JCM 12392T = NRIC 0604T. 2178 Genome sequence accession number: AZFQ00000000. 2179 16S rRNA gene accession number: AB154519. 2180 Description of Liquorilactobacillus sicerae comb. nov. 2181 Liquorilactobacillus sicerae (si’ce.rae. L. gen. n. sicerae of cider). 2182 Basonym: Lactobacillus sicerae Puertas et al. 2014, 2954VP 2183 L. sicerae cells are motile rods with polar flagella, they produce exopolysaccharides from sucrose and 2184 both malic and citric acids are utilized in the presence of glucose [205]. The genome size of the type 2185 strain is 2.49 Mbp. The mol% GC content of DNA is 37.5.

57

2186 Isolated from spoiled apple cider. 2187 The type strain is CUPV261T = CECT 8227T = KCTC 21012T. 2188 Genome sequence accession number: PRJEB5073. 2189 16S rRNA gene accession number: HG794492. 2190 Description of Liquorilactobacillus sucicola comb. nov. 2191 Liquorilactobacillus sucicola (su.ci.co’la. L. n. sucus, juice, sap; L. suff. ‐cola (from L. masc. or fem. n. 2192 incola), inhabitant, dweller; N.L. masc. n. sucicola, a sap‐dweller). 2193 Basonym: Lactobacillus sucicola Irisawa and Okada 2009, 2664VP 2194 L. sucicola cells are motile rods by means of peritrichous flagella; they do not grow in GYP broth 2195 containing 5% (w/v) NaCl [206]. The genome size of the type strain is 2.46 Mbp. The mol% GC content 2196 of DNA is 38.5. 2197 Isolated from the sap of an oak (Quercus sp.). 2198 The type strain is NRIC 0736T = DSM 21376T = JCM 15457T. 2199 Genome sequence accession number: AYZF00000000. 2200 16S rRNA gene accession number: AB433982. 2201 Description of Liquorilactobacillus uvarum comb. nov. 2202 Liquorilactobacillus uvarum (u.va′rum. L. gen. pl. n. uvarum of grapes). 2203 Basonym: Lactobacillus uvarum Mañes‐Lázaro et al. 2008, 2129VL 2204 L. uvarum cells are motile rods; they grow at pH 4.5 and 8 but not at pH 3.3. They produce 2205 exopolysaccharide from sucrose [207]. The genome size of the type strain is 2.69 Mbp. The mol% GC 2206 content of DNA is 36.9. 2207 Isolated from from Bobal grape musts. 2208 The type strain is 8T = Lb8T= CECT 7335T = DSM 19971T = JCM 16870T. 2209 Genome sequence accession number: AZEG00000000. 2210 16S rRNA gene accession number: AY681126. 2211 Description of Liquorilactobacillus vini comb. nov. 2212 Liquorilactobacillus vini (vi’ni. L. gen. n. vini of wine). 2213 Basonym: Lactobacillus vini Rodas et al. 2006, 516VP 2214 The cells are motile rods, they do not produce exopolysaccharide from sucrose, but they utilize citric 2215 and malic acids [208]. L. vini was the first organism for which metabolism of pentoses via the pentose 2216 phosphate pathway to lactate as sole end product was described [18]. The metabolism for 2217 homofermentative metabolism of pentoses was initially described for strains later classified as L. vini 2218 [18, 209]. The genome size of the type strain is 2.24 Mbp. The mol% GC content of DNA is 37.5. 2219 Isolated from fermenting Spanish grape must and from bioethanol industrial processes in different 2220 distilleries of Brazil. 2221 The type strain is Mont 4T = CECT 5924T = DSM 20605T = JCM 14280T. 2222 Genome sequence accession number: AYYX00000000.

58

2223 16S rRNA gene accession number: AJ576009. 2224 DESCRIPTION OF LIGILACTOBACILLUS GEN. NOV. 2225 Ligilactobacillus (Li.gi.lac.to.ba.cil'lus. L. v. ligare to tie, unite; N.L. masc. n. Lactobacillus a bacterial 2226 genus name; N.L. masc. n. Ligilactobacillus a lactobacillus with a host‐associated life style). 2227 Species of Ligilactobacillus are homofermentative, their mol% GC content is between 32.5 and 43.3. 2228 Several Ligilactobacillus species include strains that are motile. Most Ligilactobacillus species have 2229 been isolated from animals and humans and are adapted to vertebrate hosts. Several strains of 2230 Ligilactobacillus express urease, this enzyme is the most powerful bacterial tool to withstand gastric 2231 acidity; in lactobacilli, urease activity is associated with a vertebrate host adapted lifestyle [210, 211]. 2232 Several Ligilactobacillus species also commonly occur in fermented foods and are used commercially 2233 as starter cultures or cultures. 2234 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Ligilactobacillus is 2235 provided in Figure S6J. 2236 The type species is Ligilactobacillus salivarius comb. nov.; Ligilactobacillus was previously referred to 2237 as L. salivarius group. 2238 Description of Ligilactobacillus salivarius comb. nov. 2239 Ligilactobacillus salivarius (sa.li.va’ri.us. L. masc. adj. salivarius salivary). 2240 Basonym: Rogosa et al. 1953, 691 (Approved Lists); emend. Li et al. 2006 2241 L. salivarius strains require pteroylglutamic acid and niacin for good growth. Riboflavin is also markedly 2242 stimulatory. Good growth does not take place in media unless polyoxyethylene sorbitan monooleate 2243 (Tween 80) is added [61, 212]. The genome size of the type strains is 1.98 Mbp. The mol% GC content 2244 of DNA is 37.5. 2245 Isolated from the mouth and intestinal tract of humans, cats, hamsters, chickens and swine, and from 2246 dairy products; the species shows no adaptation to specific hosts [213]. 2247 The type strain is H066T = ATCC 11741T= CCUG 31453T = CIP 103140T = DSM 20555T = JCM 1231T = LMG 2248 9477T = NRRL B‐1949T. 2249 Genome accession number: AYYT00000000. 2250 16S rRNA gene accession number: AF089108. 2251 Description of Ligilactobacillus acidipiscis comb. nov. 2252 Ligilactobacillus acidipiscis (a.ci.di.pis’cis. L. masc. adj. acidus sour; L. n. piscis fish; N.L. gen. n. 2253 acidipiscis of a sour fish, an isolation source of strains of this species). 2254 Basonym: Lactobacillus acidipiscis Tanasupawat et al. 2000, 1481VP. The species includes strains 2255 previously designated as L. cypricasei [214] 2256 L. acidipiscis strains grow in 10% NaCl; some strains grow in the presence of 12% NaCl. They show no 2257 reaction in litmus milk and do not form slime from sucrose. Niacin and calcium pantothenate are 2258 required for growth [215]. The genome size of the type strain is 2.33 Mbp. The mol% GC content of 2259 DNA is 39.1. 2260 Isolated from fermented fish (pla‐ra and pla‐chom) in Thailand but also found in dairy products, soy 2261 sauce mash, table olives, sake starter, tropical grasses, forage crops, bee pollen, and Chinese DaQu, a 2262 saccharification starter for production of vinegar and liquor from cereals.

59

2263 The type strain is FS60‐1T = CCUG 46556T = CIP 106750T = DSM 15836T = HSCC 1411T = JCM 10692T = 2264 NBRC 102163T = NRIC 0300T = PCU 207T = TISTR 1386T. 2265 Genome sequence accession number: AZFI00000000. 2266 16S rRNA gene accession number: AB023836. 2267 Description of Ligilactobacillus agilis comb. nov. 2268 Ligilactobacillus agilis (a’gi.lis. L. masc. adj. agilis agile, motile). 2269 Basonym: Lactobacillus agilis Weiss et al. 1982, 266VP (Effective publication: Weiss et al. 1981, 252) 2270 L. agilis strains are motile with peritrichous flagella; motility is easily demonstrated in MRS broth [174]. 2271 The genome size of the type strain is 2.06 Mbp. The mol% GC content of DNA is 41.7. 2272 Isolated from municipal sewage; L. agilis is the dominant species in the pigeon crops and it is also 2273 found in the gut and cecum of birds, human gut and vagina, porcine intestinal mucin and fermented 2274 food products such as masau fruits, Nigerian ogi, and cheese. 2275 The type strain is CIP 101264T = CCUG 31450T = DSM 20509T = JCM 1187T = LMG 9186T = NRRL B‐ 2276 14856T. 2277 Genome sequence accession number: AYYP00000000. 2278 16S rRNA gene accession number: M58803. 2279 Description of Ligilactobacillus animalis comb. nov. 2280 Ligilactobacillus animalis (a.ni.ma′lis. L. gen. n. animalis, of an animal). 2281 Basonym: Lactobacillus animalis Dent and Williams 1983, 439VP; Effective publication: Dent and 2282 Williams 1982, 384 2283 L. animalis strains grow at 45°C, cells in exponential growth phase occur singly or in pairs [216]. The 2284 genome size of the type strain is 1.89 Mbp. The mol% GC content of DNA is 41.1 2285 Isolated from dental plaques and intestines of animals. 2286 The type strain is 535T = ATCC 35046T = CCUG 33906T = CIP 103152T = DSM 20602T = IFO (now NBRC) 2287 15882T = JCM 5670T = LMG 9843T = NCIMB 13278T (formerly NCDO 2425T) = NRRL B‐14176T. 2288 Genome sequence accession number: AYYW00000000. 2289 16S rRNA gene accession number: AB326350. 2290 Description of Ligilactobacillus apodemi comb. nov. 2291 Ligilactobacillus apodemi (a.po.de′mi. N.L. gen. n. apodemi, of Apodemus speciosus, the field mouse 2292 from which the organism was first isolated). 2293 Basonym: Lactobacillus apodemi Osawa et al. 2006, 1695VP 2294 L. apodemi strains are non‐motile, they are tannase‐positive and they produce gallic acid from tannic 2295 acid but they do not convert gallic acid to pyrogallol [217]. The genome size of the type strain is 2.10 2296 Mbp. The mol% GC content of DNA is 38.6. 2297 Isolated from the faeces of a wild mouse faeces. 2298 The type strain is ASB1T = CIP 108913T = DSM 16634T = JCM 16172T. 2299 Genome sequence accession number: AZFT00000000.

60

2300 16S rRNA gene accession number: AJ871178. 2301 Description of Ligilactobacillus araffinosus sp. nov. 2302 Ligilactobacillus araffinosus (a.raf.fi.no’sus. Gr. pref. a not; N.L. masc. adj. raffinosus of raffinose; N.L. 2303 masc. adj. araffinosus, not fermenting raffinose). 2304 Basonym: Lactobacillus aviarius subsp. araffinosus Fujisawa et al. 1985, 223VP; Fujisawa et al. 1986, 2305 (Effective publication: Fujisawa et al., 1984, 419). Placement of L. araffinosus in a separate species is 2306 supported by ANI values and digital DNA‐DNA hybridization [10]. The availability of the genome 2307 sequences of the type strains of both subspecies revealed that they are only distantly related with an 2308 ANI value of 88.98%, substantially below the 95‐96% threshold recognised for the species level. 2309 Furthermore, their core nucleotide identity (CNI) [10] is 91.1, which is below the 94% threshold at 2310 which two strains are allocated to the same species. Finally, their in silico DDH value is 37.80, which 2311 additionally supports that these two subspecies should be recognised as different species [10]. 2312 Cells are Gram‐ positive, non‐motile, non‐spore‐forming rods with rounded ends, usually occurring 2313 singly or in short chains. L. araffinosus strains ferment trehalose and cellobiose, they do not produce 2314 acid from galactose, lactose, melibiose and raffinose [51]. The genome size of the type strain is 1.48 2315 Mbp. The mol% GC content of DNA is 38.1. 2316 Isolated from the intestine and faeces of birds. 2317 The type strain is ML2T = ATCC 43235T= DSM 20653T = CCUG 32231T = CIP 103145T = JCM 5667T 2318 Genome sequence accession number: AYYZ00000000. 2319 16S rRNA gene accession number: AB289043. 2320 Description of Ligilactobacillus aviarius comb. nov. 2321 Ligilactobacillus aviarius (a.vi.a’ri.us. L. masc. adj. aviarius, pertaining to birds). 2322 Basonym: Lactobacillus aviarius Fujisawa et al. 1985, 223VP; Fujisawa et al. 1986; Effective publication: 2323 Fujisawa et al., 1984, 419 2324 The cells are non‐motile rods with rounded ends, occurring singly or in short chains. The final pH of 2325 glucose broth is 3.9 ‐ 4.0. This species is strictly anaerobic [51]. The genome size of the type strain is 2326 1.68 Mbp. The mol% GC content of DNA is 40.1. 2327 Isolated from the intestine and faeces of birds. 2328 The type strain is 75T = ATCC 43234T = DSM 20655T = CCUG 32230T = CIP 103144T = JCM 5666T = LMG 2329 10753T = NBRC 102162T. 2330 Genome sequence accession number: AYZA00000000. 2331 16S rRNA gene accession number: M58808. 2332 Description of Ligilactobacillus ceti comb. nov. 2333 Ligilactobacillus ceti (ce′ti. L. gen. n. ceti, of a whale). 2334 Basonym: Lactobacillus ceti Vela et al. 2008, 893VP 2335 Original characteristics of the species are described in [218]. The genome size of the type strain is 1.40 2336 Mbp. The mol% GC content of DNA is 33.7. 2337 Isolated from the lungs of a beaked whale. 2338 The type strain is 142‐2T = CCUG 53626T = DSM 22408T = CECT 7185T = JCM 15609T.

61

2339 Genome accession number: JQBZ00000000. 2340 16S rRNA gene accession number: AM292799. 2341 Description of Ligilactobacillus equi comb. nov. 2342 Ligilactobacillus equi (e′qui. L. gen. n. equi, of the horse). 2343 Basonym: Lactobacillus equi Morotomi et al. 2002, 214VP 2344 Strains of this species are non‐motile rods and some of them contain filamentous cells [219]. The 2345 genome size of the type strain is 2.30 Mbp. The mol% GC content of DNA is 39.0. 2346 Isolated from faeces of horses. 2347 The type strain is YIT 0455T = ATCC BAA‐261T = DSM 15833T = CCUG 47129T = JCM 10991T. 2348 Genome accession number: AZFH00000000. 2349 16S rRNA gene accession number: AM292799. 2350 Description of Ligilactobacillus faecis comb. nov. 2351 Ligilactobacillus faecis (fae’cis. L. gen. n. faecis of faeces). 2352 Basonym: Lactobacillus faecis Endo et al. 2013, 4505VP. 2353 Original characteristics of the species described in [220]. The mol% GC content of DNA is 41.1. 2354 Isolated from faeces of a jackal (Canis mesomelas) and raccoons (Procyron lotor). 2355 The type strain is AFL13‐2T = JCM 17300T = DSM 23956T. 2356 Genome accession number: not available at time of publication 2357 16S rRNA gene accession number: AB812750. 2358 Description of Ligilactobacillus hayakitensis comb. nov. 2359 Ligilactobacillus hayakitensis (ha.ya.ki.ten′sis. N.L. masc. adj. hayakitensis, of Hayakita, the name of 2360 the area where the bacterium was originally isolated). 2361 Basonym: Lactobacillus hayakitensis Morita et al. 2007, 2838VP 2362 Original characteristics of the species are described in [221]. The genome size of the type strain is 1.70 2363 Mbp. The mol% GC content of DNA is 34.1. 2364 Isolated from the faeces of a thoroughbred as predominant species in the intestinal microbiota. 2365 The type strain is KBL13T = DSM 18933T = JCM 14209T. 2366 Genome accession number: AZGD00000000. 2367 16S rRNA gene accession number: AB267406. 2368 Description of Ligilactobacillus murinus comb. nov. 2369 Ligilactobacillus murinus (mu.ri’nus. L. adj. murinus of mice). 2370 Basonym: Lactobacillus murinus Hemme et al., 1982, 384VP. 2371 L. murinus strains are non‐motile rods which slowly ferment ribose and arabinose. L‐LDH is activated 2372 by FDP and Mn2+. They do not hydrolyze urea and hippurate; they decarboxylate malate. Riboflavin is 2373 a required growth factor [222]. The genome size of the type strain is 2.20 Mbp. The mol% GC content 2374 of DNA is 40.1.

62

2375 Isolated from the intestinal tract of mice and rats and from sourdough. 2376 The type strain is 313T = ATCC 35020T = CCUG 33904T = CIP 104818T = CNRZ 220T = DSM 20452T = IFO 2377 (now NBRC) 14221T = JCM 1717T = LMG 14189T. 2378 Genome accession number: AYYN00000000. 2379 16S rRNA gene accession number: AJ621554. 2380 Description of Ligilactobacillus pobuzihii comb. nov. 2381 Ligilactobacillus pobuzihii (po.bu.zi’hi.i. N.L. gen. n. pobuzihii referring to the isolation of the type 2382 strain from pobuzihi, fermented cummingcordia). 2383 Basonym: Lactobacillus pobuzihii Chen et al. 2010, 1916VP 2384 Original characteristics of the species are described in [223]. The genome size of the type strain is 2.35 2385 Mbp. The mol% GC content of DNA is 37.7. 2386 Isolated from pobuzihi, fermented cummincordia, fermented fish, and traditional vinegar. 2387 The type strain is E100301T = RIFY 6501T = JCM 18084T = KCTC 13174T = NBRC 103219T. 2388 Genome accession number: JQCN00000000. 2389 16S rRNA gene accession number: AB326358. 2390 Description of Ligilactobacillus ruminis comb. nov. 2391 Ligilactobacillus ruminis (ru’mi.nis. N.L. gen. n. ruminis of rumen). 2392 Basonym: Lactobacillus ruminis Sharpe et al. 1973, 47 (Approved Lists) 2393 Strains of L. ruminis are motile by peritrichous flagella, anaerobic, and grow on surface only under 2394 reduced oxygen pressure; growth in liquid media is supported with the addition of cysteine‐HCl. 2395 Strains isolated from sewage are nonmotile and do not grow at 45°C [224]. The genome size of the 2396 type strain is 2.01 Mbp. The mol% GC content of DNA is 43.4. 2397 Isolated from rumen of cow and from sewage; also commonly found in the gut of humans, horses and 2398 pigs and bovine uterus. Genomic analyses indicated a differentiation of specific phylogenetic lineages 2399 of the species to specific vertebrate hosts [225]. 2400 The type strain is RFIT = ATCC 27780T = CCUG 39465T = CIP 103153T = DSM 20403T = JCM 1152T = LMG 2401 10756T = NBRC 102161T = NRRL B‐14853T. 2402 Genome accession number: AYYL00000000. 2403 16S rRNA gene accession number: AB326354. 2404 Description of Ligilactobacillus saerimneri comb. nov. 2405 Ligilactobacillus saerimneri (sae.rim’ne.ri. N.L. gen. masc. n. saerimneri of Saerimner, a pig occurring 2406 in Nordic mythology, because the organism was isolated from pigs). 2407 Basonym: Lactobacillus saerimneri Pedersen and Roos 2004, 1367VP 2408 Strains of this species grows aerobically in MRS agar but at a lower rate compared to anaerobic 2409 growth. They do not hydrolize esculine [226]. The genome size of the type strain is 1.69 Mbp. The 2410 mol% GC content of DNA is 42.6. 2411 Isolated from pig faeces. The habitat of L. saerimneri is the intestines of pigs, the human gut and vagina 2412 and the cecum of chicken.

63

2413 The type strain is GDA154T = CCUG 48462T = DSM 16049T = JCM 15955T = LMG 22087T. 2414 Genome accession number: AZFP00000000. 2415 16S rRNA gene accession number: AY255802. 2416 Description of Ligilactobacillus salitolerans comb nov. 2417 Ligilactobacillus salitolerans (sa.li.to’le.rans. L. masc. n. sal salt; L. pres. part. tolerans tolerating; N.L. 2418 part. adj. salitolerans salt tolerating). 2419 Basonym: Lactobacillus salitolerans Tohno et al. 2019, 967VP 2420 Characteristics of the species [227] are based on the description of one strain. The genome size of the 2421 type strain is 2.30 Mbp. The mol% GC content of DNA is 41.7. 2422 Isolated from spent mushrooms substrates. 2423 The type strain is YK43T = JCM 31331T = DSM 103433T. 2424 Genome accession number: BFFP01000000. 2425 16S rRNA gene accession number: LC127508. 2426 DESCRIPTION OF LACTIPLANTIBACILLUS GEN. NOV. 2427 Lactiplantibacillus (Lac.ti.plan.ti.ba.cil'lus. L. neut. n. lactis milk; L. fem. n. planta plant, referring to the 2428 plantarum‐group lactobacilli; L. masc. n. bacillus a rod; N.L. masc. n. Lactiplantibacillus a milk derived 2429 rodlet from the (Lactobacillus) plantarum group. 2430 Lactiplantibacillus species are Gram‐positive, non‐spore‐forming, homofermentative and non‐motile 2431 rods. Lactiplantibacillus species ferment a wide range of carbohydrates; most species metabolise 2432 phenolic acids by esterase, decarboxylase and reductase activities. Lactiplantibacillus plantarum is 2433 atypical for its pseudocatalase activity and reduction of nitrate. For discrimination between the two 2434 subspecies of L. plantarum, sequencing of the recA and cpn60 genes or AFLP profiling is necessary 2435 [228, 229]. The mol % GC content of DNA ranges between 42.9 and 48.7. 2436 Lactiplantibacillus species are isolated from many different fermented foods including fermented 2437 vegetables, meats, dairy products, and fermented cereals [58, 59], but they are also found in insect‐ 2438 associated habitats or as temporary residents of vertebrate intestinal microbiota and are 2439 characterized by a nomadic behavior [230]. L. plantarum has been widely used as a model species for 2440 metabolic, ecological, and genetic studies in lactobacilli. L. plantarum is of commercial importance as 2441 starter culture for multiple food fermentations, and is applied as probiotic culture. 2442 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Lactiplantibacillus is 2443 provided in Figure S6K. 2444 The type species is Lactiplantibacillus plantarum comb. nov.; Lactiplantibacillus was previously 2445 referred to as L. plantarum group. 2446 Description of Lactiplantibacillus plantarum comb. nov. 2447 Lactiplantibacillus plantarum (plan.ta’rum. L. gen. pl. n. plantarum of plants). 2448 Basonym: Bergey et al. 1923, 250 (Approved Lists) 2449 Previously designated as Streptobacterium plantarum [2]. Cells are nonmotile rods occurring singly, in 2450 pairs, or in short chains. Some strains reduce nitrate in limited glucose concentration and pH 6.0 or

64

2451 higher. Some strains exhibit pseudocatalase activity, or true catalase when heme is present. They 2452 require calcium pantothenate and niacin to grow [2, 231]. 2453 The species has a nomadic lifestyle; it is a dominant member of the microbiota in spontaneous 2454 vegetable and olive fermentations and also occurs in sourdough, dairy fermentations, and fermented 2455 meats [58, 59]. L. plantarum contributes to spoilage of beer and wine. L. plantarum also is part of the 2456 microbiota of insects [232], and is isolated from the human intestinal tract, particularly the oral cavity. 2457 Two subspecies are recognized: Lactiplantibacillus plantarum subsp. plantarum and Lactiplantibacillus 2458 plantarum subsp. argentoratensis. 2459 Description of Lactiplantibacillus plantarum subsp. plantarum, comb. nov. 2460 Lactiplantibacillus plantarum subsp. plantarum (plan.ta’rum. L. gen. pl. n. plantarum of plants). 2461 Basonym: Lactobacillus plantarum subsp. plantarum Bringel et al. 2005, 1633VP 2462 The description is that of the species [2, 231]. The genome size of the type strain is 3.45 Mbp. The 2463 mol% GC content of DNA is 44.2. 2464 Isolated from dairy products and dairy environments, silage, sauerkraut, pickled vegetables, sour‐ 2465 dough, cow dung, the human mouth, intestinal tract and stools, and from sewage. 2466 The type strain is ATCC 14917T = CCUG 30503T = CIP 103151T = DSM 20174T = IFO (now NBRC) 15891T 2467 = JCM 1149T = LMG 6907T = NCIMB 11974T = NRRL B‐4496T. 2468 Genome sequence accession number: AZEJ00000000. 2469 16S rRNA gene accession number: AJ965482. 2470 Description of Lactiplantibacillus plantarum subsp. argentoratensis, comb. nov. 2471 Lactiplantibacillus plantarum subsp. argentoratensis (ar.gen.to.ra.ten′sis. N.L. masc. adj. 2472 argentoratensis, of or pertaining to Argentoratus, the Roman name of the City of Strasbourg in Alsace, 2473 France). 2474 Basonym: Lactobacillus plantarum subsp. argentoratensis Bringel et al. 2005, 1633VP 2475 Strains of this species differ from L. plantarum subsp. plantarum strains due to the absence of 2476 melezitose fermentation [229]. The genome size of the type strain is 3.20 Mbp. The mol% GC content 2477 of DNA is 45. 2478 Isolated from starchy food, fermenting food of plant origin, timothy, orchardgrass and elephant grass 2479 silage, fermented Uttapam batter, fermented idli batter. 2480 The type strain is DKO 22T = CCUG 50787T = CIP 108320T = DSM 16365T = JCM 16169T. 2481 Genome sequence accession number: AZFR00000000. 2482 16S rRNA gene accession number: AJ640078. 2483 Description of Lactiplantibacillus daoliensis comb. nov. 2484 Lactiplantibacillus daoliensis (dao.li.en’sis. N.L. masc. adj. daoliensis, pertaining to Daoli, a district in 2485 Harbin city, China). 2486 Basonym: Lactobacillus daoliensis Liu and Gu 2019, 3258VP 2487 Characteristics are similar to L. pingfangensis but the strain does not grow at 37°C [233]. The genome 2488 size of the type strain is 2.63 Mbp. The mol% GC content of DNA is 43.7.

65

2489 Isolated from fermented Chinese cabbage. 2490 The type strain is 116‐1AT = LMG 31171T = NCIMB 15181T = CCM 8934T. 2491 Genome sequence accession number: BJDH00000000. 2492 16S rRNA gene accession number: LC438516. 2493 Description of Lactiplantibacillus daowaiensis comb. nov. 2494 Lactiplantibacillus daowaiensis (dao.wai.en’sis. N.L. masc. adj. daowaiensis, pertaining to Daowai, a 2495 district in Harbin city, China). 2496 Basonym: Lactobacillus daowaiensis Liu and Gu 2019, 3258VP 2497 Characteristics are similar to L. pingfangensis but the strain does not grow at 37°C [233]. The genome 2498 size of the type strain is 2.85 Mbp. The mol% GC content of DNA is 44.0. 2499 Isolated from fermented Chinese cabbage. 2500 The type strain is 203‐3T =LMG 31172T =NCIMB 15183T = CCM 8933T. 2501 Genome sequence accession number: BJDJ00000000. 2502 16S rRNA gene accession number: LC438517. 2503 Description of Lactiplantibacillus dongliensis comb. nov. 2504 Lactiplantibacillus dongliensis (dong.li.en’sis. N.L. masc. adj. dongliensis pertaining to a district in 2505 Harbin, China). 2506 Basonym: Lactobacillus dongliensis Liu and Gu 2019, 3259VP 2507 Characteristics are similar to L. pingfangensis but the type strain of L. dongliensis also f.erments ribose 2508 [233]. The genome size of the type strain is 3.11 Mbp. The mol% GC content of DNA is 44.7. 2509 Isolated from fermented Chinese cabbage. 2510 The type strain is 218‐3T = LMG 31173T = NCIMB 15184T = CCM 8932T. 2511 Genome sequence accession number: BJDK00000000 2512 16S rRNA gene accession number: LC438518. 2513 Description of Lactiplantibacillus fabifermentans comb. nov. 2514 Lactiplantibacillus fabifermentans (fa.bi.fer.men’tans. L. fem. n. faba a bean; L. pres. part. fermentans 2515 fermenting; N.L. part. adj. fabifermentans fermenting beans). 2516 Basonym: Lactobacillus fabifermentans De Bruyne et al. 2009, 10VP 2517 Cells are non‐motile long rods, usually singly, in pairs or in short chains. Colonies are circular with a 2518 convex elevation and an entire margin. They grow at 37°C, pH 3.9 and with 6% NaCl [198]. The genome 2519 size of the type strain is 3.28 Mbp. The mol% GC content of DNA is 45.0. 2520 Isolated from cocoa bean heap fermentation, fermented grapes, and fermented cereals. 2521 The type strain is R‐34115T = DSM 21115T = LMG 24284T. 2522 Genome sequence accession number: AYGX00000000. 2523 16S rRNA gene accession number: AM905388.

66

2524 Description of Lactiplantibacillus herbarum comb. nov. 2525 Lactiplantibacillus herbarum (her.ba’rum. L. gen. pl. n. herbarum, of herbs). 2526 Basonym: Lactobacillus herbarum Mao et al. 2015, 4685VP 2527 Cells are non‐motile rods, usually singly, in pairs or in short chains. The contains meso‐ 2528 diaminopimelic acid, alanine, glutamic acid, galactose and an unidentified sugar. They produce acetoin 2529 from pyruvate. L. herbarum can be distinguished from related species on the basis of sucrose 2530 fermentation (it does not ferment sucrose) and growth temperature (it cannot grow at 37°C) [234]. 2531 The genome size of the type strain is 2.90 Mbp. The mol% GC content of DNA is 43.5. 2532 Isolated from fermented radish. 2533 The type strain is TCF032‐E4T = CCTCC AB2015090T = DSM 100358T. 2534 Genome sequence accession number: LFEE00000000. 2535 16S rRNA gene accession number: NR_145899. 2536 Description of Lactiplantibacillus modestisalitolerans comb. nov. 2537 Lactiplantibacillus modestisalitolerans (mo.des.ti.sa.li.to’le.rans. L. masc. adj. modestus moderate; L. 2538 masc. n. sal salis salt; L. pres. part. tolerans tolerating; N.L. part. adj. modestisalitolerans moderately 2539 salt tolerating). 2540 Basonym: Lactobacillus modestisalitolerans Miyashita et al. 2015, 2489VP 2541 Cells are non‐motile, non‐spore‐forming, facultatively anaerobic rods. They grow at 15‐40°C, pH 3.5‐ 2542 7.5, and 0‐9% NaCl. They produce both lactic acid isomers. They hydrolyse aesculin, are tellurite and 2543 bile‐aesculin tolerant and convert arginine to ornithine [235]. The genome size of the type strain is 2544 2.75 Mbp. The mol% GC content of DNA is 48.6. 2545 Isolated from Pla‐som (fermented fish). 2546 The type strain is NB446T = NBRC 107235T = BCC 38191T. 2547 Genome sequence accession number: BJEA00000000. 2548 16S rRNA gene accession number: AB907192. 2549 Description of Lactiplantibacillus mudanjiangensis comb. nov. 2550 Lactiplantibacillus mudanjiangensis (mu.dan.ji.ang.en’sis. N.L. masc. adj. mudanjiangensis pertaining 2551 to the Mudanjiang River, a river flowing through the Heilongjiang province of China where the 2552 bacterium was isolated). 2553 Basonym: Lactobacillus mudanjiangensis Gu et al. 2013, 4703VP 2554 Cells are facultatively anaerobic rods occurring singly. Growth is observed at 30 and 37°C and pH 4, 2555 they are resistant to 6% (w/v) NaCl [176]. The genome size of the type strain is 3.58 Mbp. The mol% 2556 GC content of DNA is 42.9. 2557 Isolated from fermented Chinese cabbage [176] and fermented carrot juice [236] . 2558 The type strain is 11050T = LMG 27194T = CCUG 62991T 2559 Genome sequence accession number: BJDY00000000. 2560 16S rRNA gene accession number: HF679037.

67

2561 Description of Lactiplantibacillus nangangensis comb. nov. 2562 Lactiplantibacillus nangangensis (nan.gang.en’sis. N.L. masc. adj. nangangensis, pertaining to 2563 Nangang, a district in Harbin city, China). 2564 Basonym: Lactobacillus nangangensis Liu and Gu 2019, 3258VP 2565 Characteristics are similar to L. pingfangensis but the strain does not grow at 37°C [233]. The genome 2566 size of the type strain is 2.90 Mbp. The mol% GC content of DNA is 44.3. 2567 Isolated from fermented Chinese cabbage. 2568 The type strain is 381‐7T = NCIMB 15186T = CCM 8930T. 2569 Genome sequence accession number: BJDI00000000. 2570 16S rRNA gene accession number: LC438520 2571 Description of Lactiplantibacillus paraplantarum comb. nov. 2572 Lactiplantibacillus paraplantarum (pa.ra.plan.tar’um. Gr. prep. para resembling; N.L. gen. n. 2573 plantarum, a species epithet; N.L. gen. pl. n. paraplantarum, resembling L. plantarum). 2574 Basonym: Lactobacillus paraplantarum Curk et al. 1996, 598VP 2575 The cells are non‐motile rods, usually singly, in pairs and sometimes in short chains. They grow at pH 2576 5 and 7 and they tolerate NaCl up to a concentration of 8% [237]. The genome size of the type strain 2577 is 3.40 Mbp. The mol% GC content of DNA is 43.7. 2578 Isolated as spoilage organisms from beer and from human faeces. They are also found in grape 2579 marmalade, dairy products, jangajji (a Korean fermented food), fermented vegetables, fermented 2580 fruits, fermented dates, rice bran pickles, silage, cocoa beans, fermented sourdough, fermented slurry, 2581 faecal microbiota of healthy dogs, traditional fura processing, wine and sow milk. 2582 The type strain is CST 10961T = ATCC 700211T = CCUG 35983T = CIP 104668T = CNRZ 1885T = CST 10961T 2583 = DSM 10667T = JCM 12533T = LMG 16673T = NRRL B‐23115T. 2584 Genome sequence accession number: AZEO00000000. 2585 16S rRNA gene accession number: AJ306297. 2586 Description of Lactiplantibacillus pentosus comb. nov. 2587 Lactiplantibacillus pentosus (pen.to′sus. N.L. masc. adj. pentosus, of pentose, pertaining to pentoses). 2588 Basonym: Lactobacillus pentosus (ex Fred et al. 1921) Zanoni et al. 1987, 339VP 2589 The cells are non‐motile straight rods and produce acid and clot in litmus milk [238]. The genome size 2590 of the type strain is 3.65 Mbp. The mol% GC content of DNA is 46.3. 2591 Isolated from diverse sources including corn silage, fermenting olives, sewage, fermented mulberry 2592 leaf powders, fermented teas, glutinous rice dough, corn noodles, chili sauce, mustard pickles, stinky 2593 tofu, dairy products, mustard pickle, fermented idli batter, tempoyak, human vagina, human stools, 2594 and sourdoughs. 2595 The type strain is 124‐2T = ATCC 8041T = CCUG 33455T = CIP 103156T = DSM 20314T = JCM 1558T = LMG 2596 10755T = NCAIM B.01727T = NCCB 32014T = NCIMB 8026T (formerly NCDO 363) = NRRL B‐227T = NRRL 2597 B‐473T. 2598 Genome sequence accession number: AZCU00000000.

68

2599 16S rRNA gene accession number: D79211. 2600 Description of Lactiplantibacillus pingfangensis comb. nov. 2601 Lactiplantibacillus pingfangensis (ping.fang.en’sis. N.L. masc. adj. pingfangensis, pertaining to a 2602 district in Harbin city, China). 2603 Basonym: Lactobacillus pingfangensis Liu and Gu 2019, 7VP 2604 Growth is observed at 30 and 37 but not at 45°C; DL‐lactic acid is produced from a wide range of 2605 hexoses and disaccharides but not from pentoses [233]. The genome size of the type strain is 2.90 2606 Mbp; the mol% GC content of DNA is 44.2. 2607 Isolated from fermented Chinese cabbage. 2608 The type strain is 382‐1T = LMG 31176T = NCIMB 15187T = CCM 8935T. 2609 Genome sequence accession number: BJDG00000000. 2610 16S rRNA gene accession number: LC438521. 2611 Description of Lactiplantibacillus plajomi comb. nov. 2612 Lactiplantibacillus plajomi (pla.jom’i. N.L. gen. n. plajomi of Pla‐jom, referring to the isolation of the 2613 type strain from a traditional fermented fish product in Thailand). 2614 Basonym: Lactobacillus plajomi Miyashita et al. 2015, 2488VP 2615 Cells are non‐motile, facultatively anaerobic rods. They grow at 15‐37°C, at pH 4.0‐7.5 and with 0‐8% 2616 NaCl. They are positive for Voges–Proskauer test, tellurite tolerance, bile‐aesculin tolerance test and 2617 deamination of arginine [235]. The genome size of the type strain is 2.76 Mbp. The mol% GC content 2618 of DNA is 48.7 2619 Isolated from Pla‐jom (fermented fish) collected in Yasothon, Thailand. 2620 The type strain is NB53T = NBRC 107333T = BCC 38054T. 2621 Genome sequence accession number: BJDZ00000000. 2622 16S rRNA gene accession number: AB907190. 2623 Description of Lactiplantibacillus songbeiensis comb. nov. 2624 Lactiplantibacillus songbeiensis (song.bei.en’sis. N.L. masc. adj. songbeiensis pertaining to Songbei, a 2625 district in Harbin city, China). 2626 Basonym: Lactobacillus songbeiensis Liu and Gu 2019, 3259VP 2627 Characteristics are similar to L. pingfangensis but the type strain of L. songbeiensis also ferments 2628 ribose [233]. The genome size of the type strain is 3.03 Mbp. The mol% GC content of DNA is 44.4. 2629 Isolated from fermented Chinese cabbage. 2630 The type strain is 398‐2T = LMG 31174T = NCIMB 15189T = CCM 8931T. 2631 Genome sequence accession number: BJDL00000000. 2632 16S rRNA gene accession number: LC438523. 2633 Description of Lactiplantibacillus xiangfangensis comb. nov. 2634 Lactiplantibacillus xiangfangensis (xi.ang.fang.en′sis. N.L. masc. adj. xiangfangensis, pertaining to 2635 Xiangfang, a district of Harbin city in China).

69

2636 Basonym: Lactobacillus xiangfangensis Gu et al. 2012, 860VP 2637 Cells are non‐spore‐forming, facultatively anaerobic rods. They grow at 30 and 37°C [239]. The 2638 genome size of the type strain is 2.99 Mbp. The mol% GC content of DNA is 45.1. 2639 Isolated from pickle and sourdough. 2640 The type strain is 3.1.1T = LMG 26013T = NCIMB 14687T. 2641 Genome sequence accession number: JQCL00000000. 2642 16S rRNA gene accession number: HM443954. 2643 HETEROFERMENTATIVE LACTOBACILLACEAE 2644 DESCRIPTION OF FURFURILACTOBACILLUS GEN. NOV. 2645 Furfurilactobacillus (Fur.fu.ri.lac.to.ba.cil’lus. L. masc. n. furfur bran, relating to the origin of 2646 furfurilactobacilli from cereal fermentations; N.L. masc. n. Lactobacillus a bacterial genus name; N.L. 2647 masc. n. Furfurilactobacillus a lactobacillus from bran). 2648 Heterofermentative and aerotolerant. Growth is observed at 15 and 37°C but not at 45°C. The two 2649 species in the genus with genome sequences available have a genome size of 2.9 – 3.0 Mbp and a 2650 mol% GC content of DNA of 43 – 44%. Species in the genus were isolated from sourdough or spoiled 2651 beer and have an exceptional capacity to metabolize phenolic compounds [240, 241]. The ecology of 2652 the genus remains largely unexplored but appears to be similar to the nomadic lifestyle of L. 2653 plantarum. 2654 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Lactiplantibacillus is 2655 provided in Figure S6L. 2656 The type species of the genus is Furfurilactobacillus rossiae comb. nov.; Furfurilactobacillus was 2657 previously referred to as L. rossiae group. 2658 Description of Furfurilactobacillus rossiae comb. nov. 2659 Furfurilactobacillus rossiae (ros’si.ae. N.L. gen. n. rossiae of Rossi, named in recognition of Jone Rossi, 2660 a microbiologist working at the University of Perugia). 2661 Basonym: Lactobacillus rossiae Corsetti et al. 2005, 39VP. The species was initially named “L. rossii” 2662 F. rossiae grows at 15°C but not at 45°C [242]. The genome size of the type strain is 2.87 Mbp. The 2663 mol% GC content of DNA is 43.3. 2664 Isolated from wheat sourdough and from related cereal fermentations, beer, fruit, and fecal samples 2665 of children and swine. Owing to its capacity for metabolism of phenolic compounds and flavonoids, it 2666 was used experimentally as starter culture for cactus pear fermentation [243]. 2667 The type strain is CS1T = ATCC BAA‐822T = DSM 15814T = JCM 16176T. 2668 Genome sequence accession number: AZFF00000000. 2669 16S rRNA gene accession number: AJ564009. 2670 Description of Furfurilactobacillus curtus comb. nov. 2671 Furfurilactobacillus curtus (cur’tus. L. masc. adj. curtus short, referring to the short cell morphology of 2672 the type strain). 2673 Basonym: Lactobacillus curtus Asakawa et al. 2017, 3905VP

70

2674 It grows over a wide pH range (pH 3.5 – 8.5) and at 15°C but not at 45°C [244]. The mol% GC content 2675 of DNA is 43. 2676 Isolated from spoiled beer. 2677 The type strain is JCM 1149T = ATCC 14917T= DSM 20174 T= LMG 6907T = NCIMB 11974T = NRRL B‐ 2678 4496T. 2679 Genome sequence accession number: not available at the time of publication. 2680 16S rRNA gene accession number: LC093898. 2681 Description of Furfurilactobacillus siliginis comb. nov. 2682 Furfurilactobacillus siliginis (si.li’gi.nis. L. gen. n. siliginis, of wheat flour, referring to the origin of the 2683 type strain in wheat sourdough). 2684 Basonym: Lactobacillus siliginis Aslam et al. 2006, 2212VP 2685 This species has a narrow temperature range of growth (20 – 37°C) but a wide pH range (pH 4.0 – 8.0) 2686 [245]. The genome size of the type strain is 2.07 Mbp. The mol% GC content of DNA is 44.1. 2687 Isolated from a wheat sourdough. 2688 The type strain is M1‐212T = JCM 16155T = DSM 22696T = KCTC 3985T = NBRC 101315T. 2689 Genome sequence accession number: JQCB00000000. 2690 16S rRNA gene accession number: AB370882.

2691 DESCRIPTION OF PAUCILACTOBACILLUS GEN. NOV. 2692 Paucilactobacillus (Pau.ci.lac.to.ba.cil’lus. L. masc. adj. paucus few; N.L. masc. n. Lactobacillus a 2693 bacterial genus name; N.L. masc. n. Paucilactobacillus a lactobacillus that ferments few 2694 carbohydrates). 2695 Gram positive, rod‐shaped, catalase negative, heterofermentative, and aerotolerant. Growth is 2696 observed at between 20 and 37 °C. Several species are psychrotrophic but Paucilactobacillus suebicus 2697 grows at 45°C. Strains in this genus were predominantly isolated from fermented plant material 2698 including silage, pickles, and fruit mashes. The adaptation to hexose depleted habitats is indicated by 2699 the lack of mannitol dehydrogenase in many strains of the genus; among heterofermentative 2700 lactobacilli, this property is shared only with Secundilactobacillus that is isolated from related habitats. 2701 Paucilactobacillus species preferentially metabolise pentoses and many strains do not ferment 2702 disaccharides. The mol% GC content of DNA ranges from 35.6 to 43.5; and the genome size ranges 2703 from 1.75 to 2.57 Mbp. 2704 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Paucilactobacillus is 2705 provided in Figure S6M. 2706 The type species of the genus is Paucilactobacillus vaccinostercus comb. nov.; Paucilactobacillus was 2707 previously referred to as L. vaccinostercus group. 2708 Description of Paucilactobacillus vaccinostercus comb. nov. 2709 Paucilactobacillus vaccinostercus (vac.ci.no.ster’cus; L. masc. adj. vaccinus, from cows; L. neut. n. 2710 stercus, manure; N.L. masc. adj. vaccinostercus, from cow manure). 2711 Basonym: Lactobacillus vaccinostercus Okada et al. 1979, 439VL. Some strains of the species were 2712 previously designated as Lactobacillus durianis [246]

71

2713 Growth occurs between 15 and 40°C, pH 4.4 and 7.5, and with pentoses, glucose and maltose as 2714 carbon source [247]. The genome size of the type strain is 2.57 Mbp. The mol% GC content of DNA is 2715 43.9. 2716 Isolated from cow dung and from fermented tea leaves and fermented cereals. 2717 The type strain is X‐94T = TUA 055BT = ATCC 33310T = DSM 20634T= LMG 9215T. 2718 Genome sequence accession number: AYYY00000000. 2719 16S rRNA gene accession number: AJ621556. 2720 Description of Paucilactobacillus hokkaidonensis comb. nov. 2721 Paucilactobacillus hokkaidonensis (hok.kai.do.nen’sis. N.L. masc. adj. hokkaidonensis of Hokkaido in 2722 northern Japan from where the type strain was isolated). 2723 Basonym: Lactobacillus hokkaidonensis Tohno et al. 2013, 2529VP 2724 Growth is observed in the range of 4°C to 37°C and in the pH range of 4.0 ‐ 7.0; strains ferment 2725 pentoses, maltose and, variably, melibiose [248]. The genome size of the type strain is 2.33 Mbp. The 2726 mol% GC content of DNA is 38.1. 2727 Isolated from grass silage. 2728 The type strain is LOOC260T = JCM 18461T = DSM 26202T. 2729 Genome sequence accession number: JQCH00000000. 2730 16S rRNA gene accession number: AB721549. 2731 Description of Paucilactobacillus kaifaensis comb. nov. 2732 Paucilactobacillus kaifaensis (kai.fa.en’sis. N.L. masc. adj. kaifaensis, pertaining to Kaifa, a district in 2733 Harbin city, China). 2734 Basonym: Lactobacillus kaifaensis Liu and Gu 2019, 3259VP 2735 Growth is observed at 30 and 37 but not at 45°C. DL‐Lactic acid is produced only from ribose, xylose, 2736 maltose, arabitol and gluconate [233]. The genome size of the type strain is 1.75 Mbp; the mol% GC 2737 content of DNA is 38.0. 2738 Isolated from fermented Chinese cabbage. 2739 The type strain is 778‐3T = LMG 31177T = NCIMB 15191T = CCM 8929T. 2740 Genome sequence accession number: BJDM00000000. 2741 16S rRNA gene accession number: LC438525. 2742 Description of Paucilactobacillus nenjiangensis comb. nov. 2743 Paucilactobacillus nenjiangensis (nen.ji.ang.en’sis. N.L. masc. adj. nenjiangensis, pertaining to the 2744 Nenjiang River in the Chinese Heilongjiang province where the type strain was isolated). 2745 Basonym Lactobacillus nenjiangensis Gu et al. 2013, 4704VP 2746 The type strain ferments several pentoses, hexoses, maltose, and sucrose. Growth is not observed at 2747 45°C or below pH 4.0 [176]. The genome size of the type strain is 1.99 Mbp. The mol% GC content of 2748 DNA is 38.7. 2749 Isolated from pickle.

72

2750 The type strain is 11102T=LMG 27192T=NCIMB 14833T. 2751 Genome sequence accession number: BJEB00000000. 2752 16S rRNA gene accession number: HF679039. 2753 Description of Paucilactobacillus oligofermentans comb. nov. 2754 Paucilactobacillus oligofermentans (o.li.go.fer.men’tans, Gr. masc. adj. oligos few; L. pres. part. 2755 fermentans, fermenting; N.L. part. adj. oligofermentans, fermenting few [carbohydrates]). 2756 Basonym: Lactobacillus oligofermentans Koort et al. 2005, 2236VL 2757 Strains grow at 4 and 15°C but not at 37°C [249]. The genome size of the type strain is 1.83 Mbp. The 2758 mol% GC content of DNA is 35.6. 2759 Isolated from marinated poultry meat at the end of its shelf life, and from fermented olives. 2760 The type strain is AMKR18T = DSM 15707T = JCM 16175T = LMG 22743T. 2761 Genome sequence accession number: AZFE00000000. 2762 16S rRNA gene accession number: AY733084. 2763 Description of Paucilactobacillus suebicus comb. nov. 2764 Paucilactobacillus suebicus (su.e’bi.cus. L. masc. adj. suebicus, from Swabia, a region in the South West 2765 of Germany where the type strain was isolated). 2766 Basonym: Lactobacillus suebicus Kleynmans et al. 1989, 495VL 2767 The type strain exhibits high tolerance to acid and ethanol; growth is observed at pH 2.8 or at pH 3.3 2768 and 14% ethanol. The type strain ferments pentoses, glucose, and maltose; growth is observed at 10°C 2769 and up to 45°C for some strains [250]. The genome size of the type strain is 2.65 Mbp. The mol% GC 2770 content of DNA is 39.0. 2771 Isolated from fermented cherry mashes, from cider and silage. 2772 The type strain is I, WC‐t4‐15T = ATCC 49375T= DSM 5007T = JCM 9504T = KCTC 3549T = LMG 11408T. 2773 Genome sequence accession number: AZGF00000000. 2774 16S rRNA gene accession number: AJ575744. 2775 Description of Paucilactobacillus wasatchensis comb. nov. 2776 Paucilactobacillus wasatchensis (wa.satch.en’sis. N.L. masc. adj. wasatchensis of the Wasatch 2777 mountains in Utah, U.S.A., the origin of the type strain). 2778 Basonym: Lactobacillus wasatchensis Oberg et al. 2016, 163VP 2779 Growth is observed at 30 and 37°C but not at 45°C. In MRS, only ribose and galactose are fermented 2780 [251]. The genome size of the type strain is 1.90 Mbp. The mol% GC content of DNA is 39.8. 2781 Isolated from spoiled cheddar cheese and from silage. 2782 The type strain is WDC04T = DSM 29958T = LMG 28678T. 2783 Genome sequence accession number: AWTT00000000. 2784 16S rRNA gene accession number: NR_147709. 2785 DESCRIPTION OF LIMOSILACTOBACILLUS GEN. NOV.

73

2786 Limosilactobacillus (Li.mo.si.lac.to.ba.cil'lus. L. masc. adj. limosus, slimy, referring to the property of 2787 most strains in the genus to produce exopolysaccharides from sucrose; N.L. masc. n. Lactobacillus a 2788 bacterial genus name; N.L. masc. n. Limosilactobacillus, a slimy lactobacillus. 2789 Gram positive, rod‐or coccoid shaped, catalase negative, heterofermentative, and anaerobic or 2790 aerotolerant. Growth is observed at 37°C and, for most species, at 45°C but not at 15°C. Strains in the 2791 genus have very small genomes ranging from 1.6 Mbp for L. equigenerosi to 2.25 Mbp for L. mucosae; 2792 the mol % GC content as calculated from whole genome shotgun sequences ranges from 38.6.1 to 2793 53.4. In comparison to other heterofermentative lactobacilli, Limosilactobacillus species ferment a 2794 relatively broad spectrum of carbohydrates, however, several species do not ferment glucose. Acid 2795 resistance is typically mediated by expression of urease, glutaminase, glutamate decarboxylase and / 2796 or arginine deiminase activities [252]. With the exception of L. fermentum and L. secaliphilus, strains 2797 in the genus were isolated from intestinal habitats, or were shown experimentally to have adapted to 2798 the intestine of vertebrate animals. Limosilactobacillus reuteri and other strains in the genus produce 2799 exopolysaccharides from sucrose to support biofilm formation on non‐secretory epithelia in the upper 2800 intestinal tract [14, 253]. In their natural habitat, Limosilactobacillus spp. generally form stable 2801 associations with Lactobacillus spp.; the same association is observed in food fermentations with 2802 Limosilactobacillus. Limosilactobacillus spp., particularly L. reuteri, are produced commercially for use 2803 as starter culture and as probiotic culture. 2804 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Limosilactobacillus is 2805 provided in Figure S6N. 2806 The type species of the genus is Limosilactobacillus fermentum comb. nov.; Limosilactobacillus was 2807 previously referred to as the Lactobacillus reuteri group. 2808 Description of Limosilactobacillus fermentum comb. nov. 2809 Limosilactobacillus fermentum (fer.men′tum. L. neut. n. fermentum which causes fermentation, 2810 leaven, ferment). 2811 Basonym: Beijerinck 1901, 233 (Approved Lists). The species includes strains 2812 previously classified as Lactobacillus cellobiosus [254] 2813 L. fermentum is the only species in Limosilactobacillus that is not adapted to the intestine of 2814 vertebrates [17]. The genome size of the type strain is 1.90 Mbp. The mol% GC content of DNA is 52.4. 2815 Occurs widely in spontaneously fermented cereals and other fermenting plant materials [58, 255], 2816 also in dairy products, manure and sewage, and the feces and vagina of humans. 2817 The type strain is F (352)T = ATCC 14931T = DSM 20052T = CIP 102980T = JCM 1173T = LMG 6902T. 2818 Genome sequence accession number: JQAU00000000. 2819 16S rRNA gene accession number: JN175331. 2820 Description of Limosilactobacillus alvi sp. nov. 2821 Limosilactobacillus alvi (al’vi. L. gen. n. alvi, of the stomach, of the digestive organs). 2822 The species was effectively but not validly published as Lactobacillus alvi Kim et al. 2011 [256]. Growth 2823 at 40°C is faster than at 37°C [256]. The mol% GC content of DNA is 42.7. 2824 Isolated from the gizzard of hens. 2825 The type strain is R54T = KCCM 90099T = LMG 31569T = JCM 17644T. 2826 Genome sequence accession number: Not available at time of publication.

74

2827 16S rRNA gene accession number: NR_118032. 2828 Description of Limosilactobacillus antri comb. nov. 2829 Limosilactobacillus antri (an’tri. L. gen. n. antri of a cave, referring to the antrum region of the 2830 stomach). 2831 Basonym: Lactobacillus antri Roos et al 2005, 81VP 2832 The genome size of the type strain is 2.24 Mbp. The mol% GC content of DNA is 51.1. 2833 Isolated from a biopsy of a healthy human gastric mucosa; strains of this species were also isolated 2834 from the intestine of other vertebrate animals [98]. 2835 The type strain is Kx146A4T = LMG 22111T = DSM 16041T= CCUG 48456T. 2836 Genome sequence accession number: AZDK00000000. 2837 16S rRNA gene accession number: AY253659. 2838 Description of Limosilactobacillus caviae comb. nov. 2839 Limosilactobacillus caviae (ca’vi.ae. N.L. gen. n. caviae of a cavia, of a guinea pig). 2840 Basonym: Lactobacillus caviae Killer et al. 2017, 2908VP 2841 Description provided by [257]. The mol% GC content of DNA is 37.7. 2842 Isolated from the oral cavity of a guinea pig. 2843 The type strain is MOZM2T = CCM 8609T = DSM 100239T = LMG 28780T. 2844 Genome sequence accession number: Not available at time of publication. 2845 16S rRNA gene accession number: KT343143. 2846 Description of Limosilactobacillus coleohominis comb. nov. 2847 Limosilactobacillus coleohominis (co.le.o.ho’mi.nis. Gr. masc. n. koleos vagina; L. gen. n. hominis of 2848 humans; N.L. gen. n. coleohominis of the vagina of humans). 2849 Basonym: Lactobacillus coleohominis Nikolaitchouk et al. 2001, 2084VP. 2850 The type strain was reported not to produce gas from glucose [258], however, the genome encodes 2851 for of the phosphoketolase pathway but lacks phosphofructokinase, the key enzyme of the 2852 Embden‐Meyerhoff pathway [14]. The genome size of the type strain is 1.72 Mbp. The mol% GC 2853 content of DNA is 41.1. 2854 Isolated from the human vagina; in addition, in human intestinal microbiota and from swine. 2855 The type strain is DSM 14060T = CCUG 44007T = CIP 106820T. 2856 Genome sequence accession number: AZEW00000000. 2857 16S rRNA gene accession number: AM113776. 2858 Description of Limosilactobacillus equigenerosi comb. nov. 2859 Limosilactobacillus equigenerosi (e.qui.ge.ne.ro’si. L. masc. n. equus, horse; L. masc. adj. generosus, of 2860 noble birth, well‐bred; N.L. gen. n. equigenerosi, from a thoroughbred horse). 2861 Basonym: Lactobacillus equigenerosi Endo et al. 2008, 917VP

75

2862 Acid tolerant and thermophilic organism; cells have a coccoid morphology [259]. The genome size of 2863 the type strain is 1.60 Mbp. The mol% GC content of DNA is 42.7. 2864 Isolated from the intestinal tract of a thoroughbred horse. 2865 The type strain is NRIC 0697T = JCM 14505T = DSM 18793T. 2866 Genome sequence accession number: AZGC00000000. 2867 16S rRNA gene accession number: AB288050. 2868 Description of Limosilactobacillus frumenti comb. nov. 2869 Limosilactobacillus frumenti (fru.men’ti. L. gen. n. frumenti from cereal). 2870 Basonym: Lactobacillus frumenti Müller et al. 2000, 2132VP 2871 Description provided in [260]. The genome size of the type strain is 1.73 Mbp. The mol% GC content 2872 of DNA is 42.6. 2873 Isolated from an industrial rye bran fermentation but also identified in the intestine of poultry and 2874 swine, and in must and wine. 2875 The type strain is TMW 1.666T = DSM 13145T = LMG 19473T. 2876 Genome sequence accession number: AZER00000000. 2877 16S rRNA gene accession number: AJ250074. 2878 Description of Limosilactobacillus gastricus comb. nov. 2879 Limosilactobacillus gastricus (gas’tri.cus. N.L. masc. adj. gastricus from Gr. adj. gastrikos of the 2880 stomach). 2881 Basonym: Lactobacillus gastricus Roos et al. 2005, 80VP 2882 Acid tolerant, anaerobic and thermophilic organisms [98]. The genome size of the type strain is 1.85 2883 Mbp. The mol% GC content of DNA is 41.6. 2884 Isolated from a biopsy of a human stomach, and from human milk. 2885 The type strain is Kx156A7T = LMG 22113T = DSM 16045T = CCUG 48454T. 2886 Genome sequence accession number: AZFN00000000. 2887 16S rRNA gene accession number: AY253658. 2888 Description of Limosilactobacillus gorillae comb. nov. 2889 Limosilactobacillus gorillae gorillae (go.ril’lae. L. gen. n. gorillae of the western lowland gorilla). 2890 Basonym: Lactobacillus gorillae Tsuchida et al. 2014, 4005VP 2891 Thermophilic organism [261]. The genome size of the type strain is 1.64 Mbp. The mol% GC content 2892 of DNA is 48.1. 2893 Isolated from the faeces of a captive gorillas and from wild western lowland gorillas. 2894 The type strain is KZ01T = JCM 19575T = DSM 28356T. 2895 Genome sequence accession number: BCAH00000000. 2896 16S rRNA gene accession number: AB904716.

76

2897 Description of Limosilactobacillus ingluviei comb. nov. 2898 Limosilactobacillus ingluviei (in.glu’vi.ei. L. gen. n. ingluviei of a crop sac). 2899 Basonym Lactobacillus ingluviei Baele et al. 2003, 135VP. The species includes strains previously named 2900 as L. thermotolerans [262]. 2901 Thermophilic species with optimal growth at 42°C and poor growth at 30°C or below [263]. The 2902 genome size of the type strain is 2.16 Mbp. The mol% GC content of DNA is 49.9. 2903 Isolated from the crop of a pigeon [263], birds (turkeys, chickens, geese) but also from cattle, carnivore 2904 faeces, and Korean rice wine (makgeolii). 2905 The type strain is KR3T = DSM 15946T = LMG 20380T = CCUG 45722T. 2906 Genome sequence accession number: AZFK00000000. 2907 16S rRNA gene accession number: AF333975. 2908 Description of Limosilactobacillus mucosae comb. nov. 2909 Limosilactobacillus mucosae (mu.co’sae. N.L. gen. n. mucosae of mucosa). 2910 Basonym: Roos et al. 2000, 256VP 2911 Many strains of the species carry a binding protein, a putative colonization factor of L. mucosae. 2912 The genome size of the type strain is 2.25 Mbp. The mol% GC content of DNA is 46.4. 2913 Isolated from the intestine of a pig [264] but also found in the intestine of other vertebrates including 2914 humans, type II sourdough, and related cereal fermentations. 2915 The type strain is S32T = CCUG 43179T = CIP 106485T = DSM 13345T = JCM 12515T. 2916 Genome sequence accession number: AZEQ00000000. 2917 16S rRNA gene accession number: AF126738. 2918 Description of Limosilactobacillus oris comb. nov. 2919 Limosilactobacillus oris (or'is. L. gen. n. oris, of the mouth). 2920 Basonym: Lactobacillus oris Farrow et al. 1988, 116VP 2921 The genome size of the type strain is 2.03 Mbp. The mol% GC content of DNA is 50.0. 2922 Isolated from the human saliva [265], and, less frequently, from other human body sites including the 2923 vagina and mother’s milk, and from foods such as corn dough and bran. 2924 The type strain is 5A1T = ATCC 49062T= CCUG 37396T = CIP 103255T = CIP 105162T = DSM 4864T = JCM 2925 7507T = JCM 11028T = LMG 9848T. 2926 Genome sequence accession number: AZGE00000000. 2927 16S rRNA gene accession number: X94229. 2928 Description of Limosilactobacillus panis comb. nov. 2929 Limosilactobacillus panis (pa’nis. L. gen. n. panis, of bread). 2930 Basonym: Lactobacillus panis Wiese et al. 1996, 452VP 2931 The genome size of the type strain is 2.01 Mbp. The mol% GC content of DNA is 48.1.

77

2932 Isolated from a type II sourdough [266], other strains of the species occur in fermenting plant material, 2933 and in the intestine of birds. 2934 The type strain is CCUG 37482T = DSM 6035T = JCM 11053T. 2935 Genome sequence accession number: AZGM00000000. 2936 16S rRNA gene accession number: X94230. 2937 Description of Limosilactobacillus pontis comb. nov. 2938 Limosilactobacillus pontis (pon’tis. L. gen. n. pontis, of a bridge, referring to BRIDGE, which was the 2939 acronym of an EU funded research project). 2940 Basonym: Vogel et al. 1994, 228VP 2941 Not all strains of L. pontis ferment glucose [267]; growth is observed at 15 and at 45°C. The genome 2942 size of the type strain is 1.67 Mbp. The mol% GC content of DNA is 43.5. 2943 Isolated from type I and type II sourdough but also as typical representatives of the intestinal 2944 microbiota of swine [76]. Other sources of isolation include silage, dairy products, mezcal 2945 fermentation and wet wheat distillers' grain. 2946 The type strain is LTH 2587T = DSM 8475T = LMG 14187T. 2947 Genome sequence accession number: AZGO00000000. 2948 16S rRNA gene accession number: X76329. 2949 Description of Limosilactobacillus reuteri comb. nov. 2950 Limosilactobacillus reuteri (reu′te.ri. N.L. gen. n. reuteri, of Reuter; named for G. Reuter, a German 2951 bacteriologist). 2952 Basonym: Lactobacillus reuteri Kandler et al. 1982, 266VL 2953 Prior to 1980, strains of the species were classified as L. fermentum Biotype II [268]. The species has 2954 been studied as model species to determine host‐adaptation of intestinal lactobacilli, and co‐ 2955 adaptation of Limosilactobacillus and Lactobacillus spp. (e.g. L. taiwanensis) that coexist in biofilms in 2956 intestinal ecosystems and preferentially different substrates [55, 56, 269]. L. reuteri is divided in host‐ 2957 adapted lineages that are equivalent to the taxonomic rank of sub‐species [269, 270] and differ in their 2958 ability to form biofilms in the mouse forestomach [271]. Few strains of L. reuteri produce the 2959 compound reutericyclin with a polyketide synthase, which is a unique ability among 2960 lactobacilli [272]. The genome size of the type strain is 1.94 Mbp. The mol% GC content of DNA is 38.6. 2961 Isolated as dominant members of the intestinal microbiota of rodents, birds, swine, and in other 2962 intestinal ecosystems; also occurs in cereal fermentations, particularly type II sourdoughs [58]. Food 2963 isolates are of intestinal origin [273]. 2964 The type strain of the species is F 275T = ATCC 23272T = DSM 20016T = JCM 1112T = LMG 9213T = LMG 2965 13557T. 2966 Genome sequence accession number: AZDD00000000. 2967 16S rRNA gene accession number: AP007281. 2968 Description of Limosilactobacillus secaliphilus comb. nov. 2969 Limosilactobacillus secaliphilus (se.ca.li.phi’lus. L. neut. n. secale rye; Gr. masc. adj. philos loving; N.L. 2970 masc. adj. secaliphilus rye‐loving).

78

2971 Basonym: Lactobacillus secaliphilus Ehrmann et al. 2007, 748VP 2972 The type strain does not ferment glucose [274]. The genome size of the type strain is 1.65 Mbp. The 2973 mol% GC content of DNA is 47.7. 2974 Isolated from a type II sourdough; although other lactobacilli in type II sourdoughs are predominantly 2975 of intestinal origin [114], the habitat of L. secaliphilus remains unknown [274]. 2976 The type strain is TMW 1.1309T = DSM 17896T = CCUG 53218T. 2977 Genome sequence accession number: JQBW00000000. 2978 16S rRNA gene accession number: AM279150. 2979 Description of Limosilactobacillus vaginalis comb. nov. 2980 Limosilactobacillus vaginalis (va.gi.na’lis. L. gen. n. vaginalis, of the vagina). 2981 Basonym: Embley et al. 1989, 368VP 2982 Description provided in [275]. The genome size of the type strain is 1.79 Mbp. The mol% GC content 2983 of DNA is 30.5. 2984 Frequently isolated as member of the microbiota of the human vagina. 2985 The type strain of the species is Lac 19T = ATCC 49540T = CCUG 31452T = CIP 105932T = DSM 5837T = 2986 JCM 9505T = LMG 12891T. 2987 Genome sequence accession number: AZGL00000000. 2988 16S rRNA gene accession number: AF243177. 2989 Proposed species in the genus Limosilactobacillus: 2990 The name “Lactobacillus timonensis” was effectively published for a species that clusters 2991 phylogenetically within the genus Limosilactobacillus [276]; however, its species description lacks 2992 essential information and a type strain was not deposited. 2993 DESCRIPTION OF SECUNDILACTOBACILLUS GEN. NOV. 2994 Secundilactobacillus (Se.cun.di.lac.to.ba.cil’lus. L. adj. secundus, second or next, following; N.L. masc. 2995 n. Lactobacillus a bacterial genus name; N.L. masc. n. Secundilactobacillus a lactobacillus that occurs 2996 in a secondary fermentation or as a spoilage organism after primary fermenters depleted hexoses and 2997 disaccharides). 2998 Gram‐positive, rod‐shaped, catalase negative, heterofermentative. Most strains grow at 15°C and 2999 some also grow at 45°C, the pH range of growth is highly variable. The genome size ranges from 1.85 3000 Mbp for S. oryzae to 3.62 Mbp for S. collinoides, the mol% GC content of DNA ranges from 41.03 – 3001 47%. Strains in the genus lead a free‐living lifestyle and were isolated as secondary fermentation or 3002 spoilage organisms from hexose‐depleted habitats including silage, beer, liquor mashes and apple 3003 cider. Metabolic properties of Secundilactobacillus spp. match adaptation to hexose‐ depleted 3004 habitats. Many strains of the genus do not reduce fructose to mannitol, a trait which differentiates 3005 Secundilactobacillus from all other heterofermentative lactobacilli except Paucilactobacillus. Many 3006 strains in the genus metabolize diols via diol‐hydratase and convert agmatine, a metabolite of arginine 3007 decarboxylation, via the agmatine deiminase pathway. Strains in the genus generally harbor genes 3008 coding for transaldolase / transketolase which mediate metabolism of pentoses to pyruvate. 3009 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Secundilactobacillus is 3010 provided in Figure S6O.

79

3011 The type species of the genus is Secundilactobacillus malefermentans comb. nov.; Secundilactobacillus 3012 was previously referred to as the Lactobacillus collinoides group. 3013 Description of Secundilactobacillus malefermentans comb. nov. 3014 Secundilactobacillus malefermentans (ma.le.fer.men’tans. L. adv. male, bad; L. part. pres. fermentans 3015 fermenting; N.L. part. adj. malefermentans badly fermenting, referring to spoiled beer). 3016 Basonym: Lactobacillus malefermentans (ex Russell and Walker 1953) Farrow et al. 1989, 371VL. The 3017 species was initially described in 1953 [277]; the species name was later revived with a new type strain 3018 [278] 3019 Strains of this species have a restricted fermentation pattern. Growth is observed 3020 between 10 and 37°C and between pH 4.1 and 8.0. The genome size of the type strain is 2.05 Mbp. 3021 The mol% GC content of DNA is 41.0. 3022 Isolated from beer. 3023 The type strain is D2 MF1T = ATCC 49373T= DSM 5705T = JCM 12497T= LMG 11455T. 3024 Genome sequence accession number: AZGJ00000000. 3025 16S rRNA gene accession number: AM113783. 3026 Description of Secundilactobacillus collinoides comb. nov. 3027 Secundilactobacillus collinoides (col.lin.o.i’des. L. masc. adj. collinus hilly; Gr. suff. eides resembling, 3028 similar; N.L. masc. adj. collinoides hill‐shaped, pertaining to colony form). 3029 Basonym: Lactobacillus collinoides Carr and Davies 1972, 470 (Approved Lists). Prior to the species 3030 description, strains of S. collinoides were referred to as L. brevis var. quinicus or L. pasteurianus var. 3031 quinicus 3032 Characteristics as described [279]; the genome size of the type strain is 3.62 Mbp. The mol% GC 3033 content of DNA is 46.1. 3034 Isolated from compost, as spoilage organisms in apple cider, table olives, dairy products, fermented 3035 durian fruit, and wines. 3036 The type strain is Cl3aT = ATCC 27612T = DSM 20515T = JCM 1123T = LMG 9194T. 3037 Genome sequence accession number: AYYR00000000. 3038 16S rRNA gene accession number: AB005893. 3039 Description of Secundilactobacillus kimchicus comb. nov. 3040 Secundilactobacillus kimchicus (kim.chi’cus. N.L. neut. n. kimchium, kimchi; L. masc. suff. ‐icus 3041 pertaining to; N.L. masc. adj. kimchicus pertaining to or isolated from kimchi, a type of sauerkraut 3042 produced in Korea). 3043 Basonym: Lactobacillus kimchicus Liang et al. 2011, 896VP 3044 Growth is observed at 15 and at 45°C and between pH 5.0 and 9.0 [280]. The genome size of the type 3045 strain is 2.59 Mbp. The mol% GC content of DNA is 46.6. 3046 The species was isolated from kimchi. 3047 The type strain is DCY51T = JCM 15530 T= KCTC 12976T. 3048 Genome sequence accession number: AZCX00000000.

80

3049 16S rRNA gene accession number: EU678893. 3050 Description of Secundilactobacillus mixtipabuli comb. nov. 3051 Secundilactobacillus mixtipabuli (mi.xti.pa’bu.li. L. masc. adj. mixtus mixed; L. neut. n. pabulum fodder; 3052 N.L. gen. n. mixtipabuli of mixed fodder, referring to the isolation of the type strain from silage). 3053 Basonym: Lactobacillus mixtipabuli Tohno et al. 2015, 1983VP 3054 Characteristics as described by [281]. The genome size of the type strain is 2.52 Mbp. The mol% GC 3055 content of DNA is 43.7. 3056 Isolated from silage. 3057 The type strain is IWT30T = JCM 19805T = DSM 28580T. 3058 Genome sequence accession number: BCMF00000000. 3059 16S rRNA gene accession number: AB894863. 3060 Description of Secundilactobacillus odoratitofui comb. nov. 3061 Secundilactobacillus odoratitofui (o.do.ra.ti.to’fu.i. L. part adj. odoratus smelly; N.L.N.L. gen. n. tofui 3062 of tofu; N.L. gen. n. odoratitofui, related to stinky tofy from which the type strain was isolated). 3063 Basonym: Lactobacillus odoratitofui Chao et al. 2010, 2905VP 3064 Characteristics of the species are as described by [282]. The genome size of the type strain is 2.76 3065 Mbp. The mol% GC content of DNA is 44.3. 3066 Isolated from fermented brine used for stinky tofu production in Taipei County, Taiwan. 3067 The type strain is YIT 11304T = BCRC 17810T = DSM 19909T = JCM 15043T. 3068 Genome sequence accession number: AZEE00000000. 3069 16S rRNA gene accession number: AB365975. 3070 Description of Secundilactobacillus oryzae comb. nov. 3071 Secundilactobacillus oryzae (o.ry’zae. L. gen. n. oryzae of rice). 3072 Basonym: Lactobacillus oryzae Tohno et al. 2013, 2961VP 3073 Growth is observed between 4 and 45°C and between pH 5.0 and 8.0 [283]. The genome size of the 3074 type strain is 1.85 Mbp. The mol% GC content of DNA is 42.8. 3075 Isolated from fermented rice grains in Tochigi, Japan. 3076 The type strain is SG293T = JCM18671T = DSM 26518T. 3077 Genome sequence accession number: BBJM00000000. 3078 16S rRNA gene accession number: AB731660. 3079 Description of Secundilactobacillus paracollinoides comb. nov. 3080 Secundilactobacillus paracollinoides (pa.ra.col.li.no’i.des. Gr. pref. para beside; N.L. masc. 3081 adj. collinoides, a species epithet; N.L. masc. adj. paracollinoides beside S. collinoides, referring to the 3082 close relationship with S. collinoides). 3083 Basonym: Lactobacillus paracollinoides Suzuki et al. 2004, 116VP. Strains of this species have been 3084 referred to as L. pastorianus prior to 2005 [284]

81

3085 Growth is observed at 15 but not at 45°C [285]. The genome size of the type strain is 3.49 Mbp. The 3086 mol% GC content of DNA is 46.8. 3087 Isolated as beer or cider spoilage organisms, and from fermented olives. 3088 The type strain is LA2T = DSM 15502T = JCM 11969T. 3089 Genome sequence accession number: AZFD00000000. 3090 16S rRNA gene accession number: AJ786665. 3091 Description of Secundilactobacillus pentosiphilus comb. nov. 3092 Secundilactobacillus pentosiphilus (pen.to.si’phi.lus. N.L. neut. n. pentosum pentose; Gr. masc. adj. 3093 philos, friend, loving; N.L. masc. adj. pentosiphilus, preferring pentoses). 3094 Basonym: Lactobacillus pentosiphilus Tohno et al. 2017, 3643VP 3095 Strains of this species do not produce acid or gas from hexoses including glucose but ferment 3096 pentoses; growth is observed between 30 and 37°C [286]. The genome size of the type strain is 2.63 3097 Mbp. The mol% GC content of DNA is 44.9. 3098 Isolated from silage. 3099 The type strain is IWT25T = JCM 31145T = DSM 102974T. 3100 Genome sequence accession number: BCMI00000000. 3101 16S rRNA gene accession number: LC085284. 3102 Description of Secundilactobacillus silagei comb. nov. 3103 Secundilactobacillus silagei (si.la’ge.i. N.L. gen. n. silagei of silage, from which the type strain was 3104 isolated). 3105 Basonym: Lactobacillus silagei Tohno et al. 2013, 4616VP 3106 Characteristics as described by [287]. The genome size of the type strain is 2.66 Mbp. The mol% GC 3107 content of DNA is 44.9. 3108 Isolated from silage. 3109 The type strain is IWT126T = JCM 19001T = DSM 27022T. 3110 Genome sequence accession number: BCMG00000000. 3111 16S rRNA gene accession number: AB786910. 3112 Description of Secundilactobacillus silagincola comb. nov. 3113 Secundilactobacillus silagincola (si.lag.in’co.la. N.L. neut. n. silagum, silage; L. masc. n. incola, 3114 inhabitant; N.L. masc. n. silagincola, living in or isolated from silage). 3115 Basonym: Lactobacillus silangincola Tohno et al. 2017, 3642VP 3116 Growth is observed between 10 and 37°C and between pH 4.0 and 7.5 [286]. The genome size of the 3117 type strain is 2.62 Mbp. The mol% GC content of DNA is 43.1. 3118 Isolated from silage. 3119 The type strain is IWT5T=JCM 31144T=DSM 102973T. 3120 Genome sequence accession number: BCMJ00000000.

82

3121 16S rRNA gene accession number: LC085283. 3122 Description of Secundilactobacillus similis comb.nov. 3123 Secundilactobacillus similis (si’mi.lis. L. masc. adj. similis, similar, as the type strain is similar to closely 3124 related species). 3125 Basonym: Lactobacillus similis Kitahara et al. 2010, 189VP 3126 S. similis grows at 15 but not at 45°C [288]. The genome size of the type strain is 3.49 Mbp. The mol% 3127 GC content of DNA is 47.0. 3128 Isolated from fermented cane molasses at alcohol plants in Thailand, and from rice wine (makgeolii). 3129 The type strain is M36T = DSM 23365T = JCM 2765T = LMG 23904T. 3130 Genome sequence accession number: AYZM00000000. 3131 16S rRNA gene accession number: AB282889. 3132 DESCRIPTION OF LEVILACTOBACILLUS GEN. NOV. 3133 Levilactobacillus (Le.vi.lac.to.ba.cil'lus. L. v. levare to lift up, release, relieve; N.L. masc. n. Lactobacillus 3134 a bacterial genus name; N.L. masc. n. Levilactobacillus a lactobacillus with leavening potential, 3135 referring to the occurrence of multiple species in the genus in type I sourdoughs that are used as sole 3136 ). 3137 Gram‐positive, rod‐shaped, catalase negative, heterofermentative. Strains grow at 15°C but not at 3138 45°C, are acid tolerant, growing generally in the pH range of 4.0 – 7.0 and produce DL‐lactic acid. The 3139 genome size ranges from 1.97 Mbp for Levilactobacillis bambusae to 3.38 Mbp for Levilactobacillis 3140 cerevisiae, the mol% GC content ranges from 46.3 – 55.9%. Strains in the genus lead a free‐living 3141 lifestyle and were isolated from sourdough or fermented vegetable products but also occur as spoilage 3142 organisms in alcoholic beverages. Strains in the genus generally harbor genes coding for transaldolase 3143 / transketolase which mediate metabolism of pentoses to pyruvate. Levilactobacillus brevis is used 3144 commercially as starter culture in food and feed applications. 3145 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Levilactobacillus is 3146 provided in Figure S6P. 3147 The type species of the genus is Levilactobacillus brevis comb. nov.; Levilactobacillus was previously 3148 referred to as L. brevis group. 3149 Description of Levilactobacillus brevis comb. nov. 3150 Levilactobacillus brevis (bre′vis. L. adj. brevis short). 3151 Basonym: (Betabacterium breve Orla‐Jensen 1919, 175) Bergey et al. 1934, 312 3152 (Approved Lists) 3153 The species was described in [2, 289]. Strains of L. brevis widely occur in vegetable and cereal 3154 fermentations and as beer‐spoilage organisms and were also isolated from insects. Niche adaptation 3155 is mediated by acquisition of [290]. The genome size of the type strain is 2.47 Mbp. The mol% 3156 GC content of DNA is 46.0. 3157 Isolated from milk, cheese, sauerkraut and rrelated vegetable fermentations, sourdough, silage, cow 3158 manure, faeces, and the mouth and intestinal tract of humans and rats. 3159 The type strain is 14, Bb14T = DSM 20054T = ATCC 14869T = JCM 1059T = LMG 6906T = LMG 7944T = 3160 NRRL B‐4527T.

83

3161 Genome sequence accession number: AZCP00000000. 3162 16S rRNA gene accession number: M58810. 3163 Description of Levilactobacillus acidifarinae comb. nov. 3164 Levilactobacillus acidifarinae (a.ci.di.fa.ri’nae. L. masc. adj. acidus sour; L. fem. n. farina; N.L. gen. n. 3165 acidifarinae of sourdough). 3166 Basonym: Lactobacillus acidifarinae Vancanneyt et al. 2005, 619VP 3167 Characteristics of the species are as described [291]. The genome size of the type strain is 2.92 Mbp. 3168 The mol% GC content of DNA is 51.5. 3169 Isolated from type I wheat sourdough and fermented rice bran. 3170 The type strain is R‐19065T = DSM 19394T = CCM 7240T = CCUG 50162T = JCM 15949T = LMG 2220T. 3171 Genome sequence accession number: AZDV00000000. 3172 16S rRNA gene accession number: AJ632158. 3173 Description of Levilactobacillus bambusae comb. nov 3174 Levilactobacillus bambusae (bam.bu’sae. N.L. gen. n. bambusae of the plant genus Bambusa from 3175 which the type strain was isolated). 3176 Basonym: Lactobacillus bambusae Guu et al. 2018, 2428VP 3177 Characteristics of the species are as described [292]; L. bambusae is more distantly related to other 3178 species in Levilactobacillus than any other species in the genus as documented by AAI, GC content and 3179 genome size. The genome size of the type strain is 1.97 Mbp. The mol% GC content of DNA is 46.3. 3180 Isolated from traditional fermented bamboo shoots. 3181 The type strain is BS‐W1T = BCRC 80970T = NBRC 112377T. 3182 Genome sequence accession number: QCXQ00000000. 3183 16S rRNA gene accession number: KX400838. 3184 Description of Levilactobacillus cerevisiae comb. nov 3185 Levilactobacillus cerevisiae (ce.re.vi’si.ae. L. gen. n. cerevisiae, of beer). 3186 Basonym: Lactobacillus cerevisiae Koob et al. 2017, 3456VP 3187 Characteristics as described [293]. The genome size of the type strain is 3.38 Mbp. The mol% GC 3188 content of DNA is 49.6. 3189 Isolated from spoiled beer. 3190 The type strain is 2301T = DSM 100836T = LMG 29073T. 3191 Genome sequence accession number: RHNN00000000. 3192 16S rRNA gene accession number: KT445896. 3193 Description of Levilactobacillus fujinensis comb. nov. 3194 Levilactobacillus fujinensis (fu.jin.en’sis. N.L. masc. adj. fujinensis, pertaining to Fujin, a county in the 3195 Heilongjiang province of China). 3196 Basonym: Lactobacillus fujinensis Long and Gu 2019, 2351VP

84

3197 Characteristics of the species are as described [158]. The genome size of the type strain is 3 Mbp. The 3198 mol% GC content of DNA is 47.4. 3199 Isolated from fermented Chinese cabbage. 3200 The type strain is 218‐6T = CCM 8908T = KCTC 21134T = LMG 31067T. 3201 Genome sequence accession number: RHNX00000000. 3202 16S rRNA gene accession number: MK110865. 3203 Description of Levilactobacillus fuyuanensis comb. nov. 3204 Levilactobacillus fuyuanensis (fu.yuan.en’sis. N.L. masc. adj. fuyuanensis, pertaining to Fuyuan, a 3205 county in the Heilongjiang province of China). 3206 Basonym: Lactobacillus fuyuanensis Long and Gu 2019, 2351VP 3207 Characteristics of the species are as described [158]. The genome size of the type strain is 2.72 Mbp. 3208 The mol% GC content of DNA is 48.6. 3209 Isolated from fermented Chinese cabbage. 3210 The type strain is 244‐4T = CCM 8906T = KCTC 21137T=LMG 31052T. 3211 Genome sequence accession number: RHNZ00000000. 3212 16S rRNA gene accession number: MK110862. 3213 Description of Levilactobacillus hammesii comb. nov. 3214 Levilactobacillus hammesii (ham.me’si.i. N.L. gen. n. hammesii of Hammes, in recognition of the 3215 scientist Walter P. Hammes, who contributed significantly to the taxonomy of lactic acid bacteria as 3216 well as the technology and microbial ecology of fermented foods). 3217 Basonym: Lactobacillus hammesii Valcheva et al. 2005, 766VP 3218 Characteristics of the species are as described [294]. Strains produce antifungal fatty acids from 3219 linoleic acid [295]. The genome size of the type strain is 2.82 Mbp. The mol% GC content of DNA is 3220 49.4. 3221 Isolated from wheat and rye sourdoughs, ryegrass silages, and a municipal biogas plant. 3222 The type strain is LP38T = TMW 1.1236T = DSM 16381T = CCUG 51325T = CIP 108387T = JCM 16170T. 3223 Genome sequence accession number: AZFS00000000. 3224 16S rRNA gene accession number: AJ632219. 3225 Description of Levilactobacillus huananensis comb. nov. 3226 Levilactobacillus huananensis (hua.nan.en’sis. N.L. masc. adj. huananensis, pertaining to Huanan, a 3227 county in the Heilongjiang province of China). 3228 Basonym: Lactobacillus huananensis Long and Gu 2019, 2350VP 3229 Characteristics are described in [158]. The genome size of the type strain is 2.29 Mbp. The mol% GC 3230 content of DNA is 47.5. 3231 Isolated from fermented Chinese cabbage. 3232 The type strain is 151‐2BT = CCM 8913T = KCTC 21129T = LMG 31063T. 3233 Genome sequence accession number: RHOC00000000.

85

3234 16S rRNA gene accession number: MK110857. 3235 Description of Levilactobacillus koreensis comb. nov. 3236 Levilactobacillus koreensis (ko.re.en’sis. N.L. masc. adj. koreensis of Korea, where the type strain was 3237 isolated). 3238 Basonym: Lactobacillus koreensis Naam Bui et al. 2011, 774VP 3239 Characteristics of the species are as described [296]. The genome size of the type strain is 2.47 Mbp. 3240 The mol% GC content of DNA is 49.6. 3241 Isolated from cabbage kimchi and from sourdough. 3242 The type strain is DCY50T = JCM 16448T = KCTC 13530T. 3243 Genome sequence accession number: AZDP00000000. 3244 16S rRNA gene accession number: FJ904277. 3245 Description of Levilactobacillus lindianensis comb. nov. 3246 Levilactobacillus lindianensis (lin.dian.en’sis. N.L. masc. adj. lindianensis, pertaining to Lindian, a 3247 county in the Heilongjiang province of China). 3248 Basonym: Lactobacillus lindianensis Long and Gu, 2019, 2349VP 3249 Characteristics are described in [158]. The genome size of the type strain is 2.33 Mbp. The mol% GC 3250 content of DNA is 49.2. 3251 Isolated from fermented Chinese cabbage. 3252 The type strain is 220‐4T = NCIMB 15163T=CCM 8902T=KCTC 21136T. 3253 Genome sequence accession number: RHOD00000000. 3254 16S rRNA gene accession number: MK110856. 3255 Description of Levilactobacillus mulengensis comb. nov. 3256 Levilactobacillus mulengensis (mu.leng.en’sis. N.L. masc. adj. mulengensis, pertaining to Muleng, a 3257 county in the Heilongjiang province of China). 3258 Basonym: Lactobacillus mulengensis Long and Gu 2019, 2352VP 3259 Characteristics of the species are as described [158]. The genome size of the type strain is 3.11 Mbp. 3260 The mol% GC content of DNA is 50.3. 3261 Isolated from fermented Chinese cabbage. 3262 The type strain is 112‐3T = CCM 8909T = KCTC 21123T = LMG 31049T. 3263 Genome sequence accession number: RHNW00000000. 3264 16S rRNA gene accession number: MK110866. 3265 Description of Levilactobacillus namurensis comb. nov. 3266 Levilactobacillus namurensis (na.mur.en’sis. N.L. masc. adj. namurensis, of the province of Namur, 3267 Belgium, the source of isolation of the type strain). 3268 Basonym: Lactobacillus namurensis Scheirlinck et al. 2007, 226VP

86

3269 Characteristics of the species are as described [297]. The genome size of the type strain is 2.48 Mbp. 3270 The mol% GC content of DNA is 52.0. 3271 Isolated from wheat sourdough and from vegetable fermentations. 3272 The type strain is DSM 19117T = CCUG 52843T = JCM 15612T = LMG 23583T. 3273 Genome sequence accession number: AZDT00000000. 3274 16S rRNA gene accession number: AM259119. 3275 Description of Levilactobacillus parabrevis comb. nov. 3276 Levilactobacillus parabrevis (pa.ra.bre’vis. Gr. pref. para beside; L. masc. adj. brevis, a species epithet; 3277 N.L. masc. adj. parabrevis beside L. brevis, referring to the close relationship with L. brevis). 3278 Basonym: Lactobacillus parabrevis Vancanneyt et al. 2006, 1556VP 3279 Characteristics of the species are as described [298]. The genome size of the type strain is 2.61 Mbp. 3280 The mol% GC content of DNA is 49.1. 3281 The species is isolated from farmhouse red Cheshire cheese, wheat sourdough, fermented vegetables, 3282 and a municipal biogas plant. 3283 The type strain is RODS‐DWT = SLB‐MAST = ATCC 53295T= LMG 11984T. 3284 Genome sequence accession number: AZCZ00000000. 3285 16S rRNA gene accession number: AM158249. 3286 Description of Levilactobacillus paucivorans comb. nov. 3287 Levilactobacillus paucivorans (pau.ci.vo’rans. L. masc. adj. paucus few, low in number; L. part. pres. 3288 vorans devouring; N.L. part. adj. paucivorans, eating few [carbohydrates], referring to the few sugars 3289 that are fermented by the type strain). 3290 Basonym: Lactobacillus paucivorans Ehrmann et al. 2010, 2356VP 3291 Characteristics of the species are as described [299]. The genome size of the type strain is 2.37 Mbp. 3292 The mol% GC content of DNA is 49.1. 3293 Isolated from a storage tank of a brewery. 3294 The type strain is TMW 1.1424T = DSM 22467T = JCM 18045T = LMG 25291T. 3295 Genome sequence accession number: JQCA00000000. 3296 16S rRNA gene accession number: FN185731. 3297 Description of Levilactobacillus senmaizukei comb. nov. 3298 Levilactobacillus senmaizukei (sen.mai.zu’ke.i. N.L. gen. n. senmaizukei of senmaizuke, a fermented 3299 pickle). 3300 Basonym: Lactobacillus senmaizukei Hiraga et al. 2008, 1627VP 3301 Characteristics of the species are as described [300]. The genome size of the type strain is 2.22 Mbp. 3302 The mol% GC content of DNA is 48.6. 3303 Isolated from senmaizuke, a fermented turnip product. 3304 The type strain is L13T = DSM 21775T = NBRC 103853T = TISTR 1847T. 3305 Genome sequence accession number: AYZH00000000.

87

3306 16S rRNA gene accession number: AB297927. 3307 Description of Levilactobacillus spicheri comb. nov. 3308 Levilactobacillus spicheri (spi’.cher.i. N.L. gen. n. spicheri of Spicher. The name honours Gottfried 3309 Spicher, a German scientist who pioneered the microbiological and biochemical characterization of 3310 sourdough fermentation). 3311 Basonym: Lactobacillus spicheri Meroth et al. 2004, 631VL 3312 Characteristics as described [301]. The genome size of the type strain is 2.75 Mbp. The mol% GC 3313 content of DNA is 55.9. 3314 Isolated from wheat and rice sourdoughs, from fermented vegetables and a municipal biogas plant. 3315 The type strain is LTH 5753T = DSM 15429T = JCM 15956T = LMG 21871T. 3316 Genome sequence accession number: AZFC00000000. 3317 16S rRNA gene accession number: AJ534844. 3318 Description of Levilactobacillus suantsaii comb. nov. 3319 Levilactobacillus suantsaii (suan.tsai’i. N.L. gen. n. suantsaii of suan‐tsai, a fermented mustard 3320 product, from which the type strain was isolated). 3321 Basonym: Lactobacillus suantsaii Liou et al. 2019, 1489VP 3322 Characteristics of the species are as described [302]. The genome size of the type strain is 2.43 Mbp. 3323 The mol% GC content of DNA is 51.1. 3324 Isolated from suan‐tsai, a traditional Taiwanese fermented mustard green. 3325 The type strain is L88T =BCRC 12945T=NBRC 113535T. 3326 Genome sequence accession number: QXIL00000000. 3327 16S rRNA gene accession number: MH730159. 3328 Description of Levilactobacillus suantsaiihabitans comb. nov. 3329 Levilactobacillus suantsaiihabitans (suan.tsai.i.ha'bi.tans. N.L. neut. n. suantsaium suan‐tsai, the name 3330 of a traditional fermented mustard green product of Taiwan; L. pres. part. habitans, inhabiting; N.L. 3331 part. adj. suantsaiihabitans inhabiting suan‐tsai). 3332 Basonym: Lactobacillus suantsaiihabitans Lin et al. 2019, 8VP 3333 Growth is observed in the range of 20 – 37°C but not at 15°C [144]. The genome size of the type strain 3334 is 2.87 Mbp. The mol% GC content of DNA is 51.8. 3335 Isolated from a fermented mustard green product. 3336 The type strain is R19T = BCRC 81129T= NBRC 113532T. 3337 Genome sequence accession number: RKLX00000000. 3338 16S rRNA gene accession number: NH810313. 3339 Description of Levilactobacillus tangyuanensis comb. nov. 3340 Levilactobacillus tangyuanensis (tang.yuan.en’sis. N.L. masc. adj. tangyuanensis, pertaining to 3341 Tangyuan, a county in the Heilongjiang province of China). 3342 Basonym: Lactobacillus tangyuanensis Long and Gu 2019, 2350VP

88

3343 Characteristics of the species are as described [158]. The genome size of the type strain is 2.19 Mbp. 3344 The mol% GC content of DNA is 49.8. 3345 Isolated from fermented Chinese cabbage. 3346 The type strain is 137‐3T = CCM 8907T = KCTC 21125T = LMG 31053T. 3347 Genome sequence accession number: RHOA00000000. 3348 16S rRNA gene accession number: MK110859. 3349 Description of Levilactobacillus tongjiangensis comb. nov. 3350 Levilactobacillus tongjiangensis (tong.ji.ang.en’sis. N.L. masc. adj. tongjiangensis, pertaining to 3351 Tongjiang, a county in the Heilongjiang province of China). 3352 Basonym: Lactobacillus tongjianensis Long and Gu 2019, 2351VP 3353 Characteristics of the species are as described [158]. The genome size of the type strain is 2.72 Mbp. 3354 The mol% GC content of DNA is 47.7. 3355 Isolated from fermented Chinese cabbage. 3356 The type strain is 218‐10T = CCM 8905T=KCTC 21135T=LMG 31055T. 3357 Genome sequence accession number: RHNY00000000. 3358 16S rRNA gene accession number: MK110863. 3359 Description of Levilactobacillus yonginensis comb. nov. 3360 Levilactobacillus yonginensis (yong.in.en’sis. N.L. masc. adj. yonginensis of Yongin, the city in Korea 3361 where the organism was isolated). 3362 Basonym: Lactobacillus yonginensis Yi et al. 2013, 3278VP 3363 Characteristics of the species are as described [303]; ginsenoside Rb1 is hydrolysed to Rd by β‐ 3364 glucosidase activity. The genome size of the type strain is 2.69 Mbp. The mol% GC content of DNA is 3365 47.8. 3366 Isolated from kimchi. 3367 The type strain is THK‐V8T = KACC 16236T = JCM 18023T = ATCC 16236T. 3368 Genome sequence accession number: RHNO00000000. 3369 16S rRNA gene accession number: JN128640. 3370 Description of Levilactobacillus zymae comb. nov. 3371 Levilactobacillus zymae (zy’mae. Gr. fem. n. zyme leaven, sourdough; N.L. gen. n. zymae of 3372 sourdough). 3373 Basonym: Lactobacillus zymae Vancanneyt et al. 2005, 619VP 3374 Characteristics of the species are as described [291]. The genome size of the type strain is 2.71 Mbp. 3375 The mol% GC content of DNA is 53.6. 3376 Isolated from a type I wheat sourdough, forages and fermented onions. 3377 The type strain is R‐18615T = DSM 19395T = CCM 7241T = CCUG 50163T = JCM 15957T = LMG 22198T. 3378 Genome sequence accession number: AZDW00000000.

89

3379 16S rRNA gene accession number: AJ632157. 3380 DESCRIPTION OF FRUCTILACTOBACILLUS GEN. NOV. 3381 Fructilactobacillus (Fruc.ti.lac.to.ba.cil’lus. L. masc. n. fructus, fruit; N.L. masc. n. Lactobacillus a 3382 bacterial genus name; N.L. masc. n. Fructilactobacillus, fruit‐loving lactobacillus, referring to the 3383 preference for growth in presence of fructose as electron acceptor). 3384 Gram positive, rod‐shaped, catalase negative, heterofermentative, and aerotolerant. Growth is 3385 observed at 15°C but not at 37°C. Strains in the genus have very small genomes ranging from 1.23 3386 Mbp for Fructilactobacillus sanfranciscensis to 1.44 Mbp for Fructilactobacillus lindneri; the mol% GC 3387 content of DNA as calculated from whole genome shotgun sequences ranges from 34.1 to 38.9. 3388 Comparable to other insect‐associated lactobacilli, strains in the genus ferment only few 3389 carbohydrates; some strains ferment only maltose and sucrose. Most strains of the species are 3390 fructophilic and use fructose as electron acceptor rather than as carbon source. Several species in the 3391 genus are core member of insect intestinal microbiota, and were isolated from insects, flowers, and 3392 spoiled or fermented foods. 3393 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Fructilactobacillus is 3394 provided in Figure S6Q. 3395 The type species of the genus is Fructilactobacillus fructivorans comb. nov.; Fructilactobacillus was 3396 previously referred to as L. fructivorans group. 3397 Description of Fructilactobacillus fructivorans comb. nov. 3398 Fructilactobacillus fructivorans (fruc.ti.vo’rans. L. masc. n. fructus, fruit; L. part. pres. vorans, eating, 3399 devouring; N.L. part. adj. fructivorans, fruit‐eating, intended to mean fructose‐devouring). 3400 Basonym: Lactobacillus fructivorans Charlton et al. 1934, 1 (Approved Lists) 3401 The type species of Fructilactobacillus was described as Lactobacillus fructivorans in 1934 [304] and 3402 includes strains that were previously described as Lactobacillus heterohiochii, Lactobacillus trichodes 3403 [305], and L. homohiochii [306]. Lactobacillus homohiochii was isolated from Saké mashes and 3404 described as homofermentative Lactobacillus species [307]. The heterofermentative L. heterohiochii 3405 (later classified as F. fructivorans comb. nov.) was isolated from the same mash. The type strain of L. 3406 homohiochii, which likely represents an organism related to Lactobacillus acetotolerans, has been lost 3407 [308]. F. fructivorans tolerates ethanol concentrations of up to 15%. The genome size of the type strain 3408 is 1.37 Mbp. The mol% GC content of DNA is 38.9. 3409 F. fructivorans is stable member of the intestinal microbiota of fruit flies [309] as well as spoiled sake 3410 mashes [58]; it was also isolated from spoiled mayonnaise, salad dressings, sourdough, dessert wines 3411 and aperitifs. 3412 The type strain is IFO (now NBRC) 13954T = ATCC 8288T = CCUG 32260T = CIP 103042T = DSM 20203T = 3413 JCM 1117T = LMG 9201T = NRRL B‐1841T. 3414 Genome sequence accession number: AZDS00000000. 3415 16S rRNA gene accession number: NR_036789. 3416 Description of Fructilactobacillus florum comb. nov. 3417 Fructilactobacillus florum (flo’rum. L. gen. pl. n. florum, of flowers, from which the type strain was 3418 isolated). 3419 Basonym: Lactobacillus florum Endo et al. 2010, 2481VP

90

3420 The species was described as composed by three fructophilic strains [310]. The genome size of the 3421 type strain is 1.35 Mbp. The mol% GC content of DNA is 41.1. 3422 Iolated from peony and bietou flowers, and from grapes and wine. 3423 The type strain is F9‐1T = DSM 22689T = JCM 16035T = NRIC 0771T. 3424 Genome sequence accession number: AYZI00000000. 3425 16S rRNA gene accession number: AB498045. 3426 Description of Fructilactobacillus ixorae comb. nov. 3427 Fructilactobacillus ixorae (i.xo’rae. N.L. gen. n. ixorae of Ixora coccinea, West Indian Jasmine as source 3428 of isolation). 3429 Basonym: Lactobacillus ixorae Techo et al. 2016, 5504VP 3430 The description is provided in [311]. The mol% GC content of DNA is 47.8. 3431 Isolated from a flower (West‐Indian jasmine). 3432 The type strain is Ru20‐1T = LMG 29008T = NBRC 111239T = PCU 346T = TISTR 2381T. 3433 Genome sequence accession number: not available at the time of publication. 3434 16S rRNA gene accession number: LC094494. 3435 Description of Fructilactobacillus lindneri comb. nov. 3436 Fructilactobacillus lindneri (lind'ne.ri. N.L. gen. n. lindneri of Lindner, recognizing the German 3437 bacteriologist Lindner). 3438 Basonym: Lactobacillus lindneri (Henneberg 1901); Back et al. 1997, 601VL Earlier isolates were 3439 referred to as Bacillus lindneri or Bacterium lindneri [312] 3440 The description is provided in [312]. The genome size of the type strain is 1.44 Mbp. The mol% GC 3441 content of DNA is 34.1. 3442 Isolated from spoiled beer and from wine. 3443 The type strain is KPAT = CIP 102983T = DSM 20690T = JCM 11027T = LMG 14528T. 3444 Genome sequence accession number: JQBT00000000. 3445 16S rRNA gene accession number: X95421. 3446 Description of Fructilactobacillus sanfranciscensis comb. nov. 3447 Fructilactobacillus sanfranciscensis (san.fran.cis.cen’sis. N.L. masc. adj. sanfranciscensis, from San 3448 Francisco). 3449 Basonym: Lactobacillus sanfranciscensis (ex Kline and Sugihara 1971) Weiss and Schillinger 1984, 503VL 3450 The species was described as Lactobacillus sanfrancisco in 1971 [313] and re‐named to Lactobacillus 3451 sanfranciscensis [314]. Isolates of F. sanfranciscensis described prior to 1978 were designated as 3452 Lactobacillus brevis subsp. lindneri [315] 3453 Virtually all isolates of the species originate from traditional sourdoughs that are used as leavening 3454 agent [114]; one isolate was obtained from agave mash [151]. The extremely small genome size of 1.2 3455 – 1.3 Mbp, the restricted carbohydrate fermentation pattern, which for includes only maltose for 3456 some strains, and the narrow pH range of growth (pH 3.9 – 6.6) [316, 317] document adaptation to a 3457 very narrow ecological niche. An insect origin of the species is suggested by culture‐independent

91

3458 analysis of the microbiota of grain beetles [318]. The genome size of the type strain is 1.23 Mbp. The 3459 mol% GC content of DNA is 34.7. 3460 The type strain is L‐12T = ATCC 27651T= DSM 20451T = LMG 16002T. 3461 Genome sequence accession number: AYYM00000000. 3462 16S rRNA gene accession number: X76327. 3463 Description of Fructilactobacillus vespulae comb. nov. 3464 Fructilactobacillus vespulae (ves’pu.lae. N.L. gen. n. vespulae of the wasp Vespula). 3465 Basonym: Lactobacillus vespulae Hoang et al. 2015, 3330VP 3466 The description is provided in [319]. The mol% GC content of DNA is 35.5. 3467 Isolated from a queen wasp. 3468 The type strain is DCY75T = KCTC 21023T = JCM 19742T. 3469 Genome sequence accession number: not available at the time of publication. 3470 16S rRNA gene accession number: JX863367.

3471 DESCRIPTION OF ACETILACTOBACILLUS GEN. NOV. 3472 Acetilactobacillus, (A.ce.ti.lac.to.ba.cil’lus. L. neut. n. acetum vinegar, referring to the isolation of the 3473 sole representative of this genus from a grain vinegar mash; N.L. masc. n. Lactobacillus a bacterial 3474 genus name; N.L. masc. n. Acetilactobacillus, a lactobacillus from vinegar). 3475 Gram‐positive, rod‐shaped, catalase negative, heterofermentative. Mesophilic, with a narrow 3476 temperature range of growth, and acid tolerant with an optimum pH of growth at 4.0. The spectrum 3477 of carbohydrates that support acid formation is unusual as it includes sugar alcohols and disaccharides 3478 but excludes most hexoses and all pentoses. The unusual substrate requirements and pH optimum for 3479 growth may reflect an ecological association with acetic acid bacteria. The sole representative of the 3480 genus was isolated from a grain vinegar mash (vinegar pei) and has a genome size of 2.33 Mbp with a 3481 mol% GC content of 41.7. 3482 The type species of the genus is Acetilactobacillus jinshanensis sp. nov. 3483 Description of Acetilactobacillus jinshanensis sp. nov. 3484 Acetilactobacillus jinshanensis (jin.shan’en.sis. N.L. masc. adj. jinshanensis, referring to Jinshan, the 3485 site of isolation in Zhenjiang province, China). 3486 The species was effectively but not validly published as Lactobacillus jinshani Yu et al. 2020 [41]. 3487 Growth is observed between 20 and 40°C with optimal growth at 35°C [41]. The optimum pH for 3488 growth is 4.0; growth occurs in the range of 3.0 – 5.0. The strain ferments several disaccharides and 3489 sugar alcohols but no pentoses. The genome size of the type strain is 2.33 Mbp. The mol% GC content 3490 of DNA is 41.7. 3491 Isolated from a grain vinegar mash. 3492 The type strain is HSLZ‐75T = CICC 6269T = JCM 33270T. 3493 Genome sequence accession number: CP034726. 3494 16S rRNA gene accession number: KT783533. 3495 DESCRIPTION OF APILACTOBACILLUS GEN. NOV.

92

3496 Apilactobacillus (A.pi.lac.to.ba.cil'lus. L. fem. n. apis bee; N.L. masc. n. Lactobacillus a bacterial genus 3497 name; N.L. masc. n. Apilactobacillus a lactobacillus from bees). 3498 Gram positive, rod‐shaped, heterofermentative. Growth is generally observed in the range of 15 – 3499 37°C; many strains grow at acidic conditions below pH 3.0. Strains in the genus have small genomes 3500 ranging from 1.42 Mbp for Apilactobacillus kosoi to 1.58 Mbp for Apilactobacillus quenuiae; the mol% 3501 GC content of DNA ranges from 30.5 to 36.4. All strains in the genus convert fructose to mannitol; 3502 strains in the genus typically ferment very few carbohydrates including the pollen and bee‐associated 3503 carbohydrates fructose, glucose, and sucrose but not maltose or pentoses. Comparable to 3504 Fructilactobacillus, Apilactobacillus has an insect‐associated lifestyle and occurs on flowers, which 3505 serve as hub for dispersal of lactobacilli, and insects [320]. In contrast to Fructilactobacillus, 3506 Apilactobacillus has adapted to bees including honeybees (A. apinorum, A. kunkeei) and wild bees (A. 3507 timberlakei, A. micheneri, A. quenuiae). In the bee and bumblebee gut, Apilactobacillus is associated 3508 with its homofermentative sister genus Bombilactobacillus. 3509 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Apilactobacillus is 3510 provided in Figure S6R. 3511 The type species of the genus is Apilactobacillus kunkeei comb. nov. Apilactobacilus was previously 3512 referred to as L. kunkeei group. 3513 Description of Apilactobacillus kunkeei comb. nov. 3514 Apilactobacillus kunkeei (kun’kee.i; N.L. gen.n. kunkeei of Kunkee, named in honor of the Californian 3515 microbiologist Ralph Kunkee). 3516 Basonym: Lactobacillus kunkeei Edwards et al. 1998, 1083VL 3517 A facultative anaerobic organism [321]; the genome size of the type strain is 1.52 Mbp. The mol% GC 3518 content of DNA is 36.4. 3519 Isolated form a sluggish grape wine fermentation but the species is typically associated with honey 3520 bees and flowers. 3521 The type strain is YH‐15T = ATCC 700308T= DSM 12361T = JCM 16173T. 3522 Genome sequence accession number: AZCK00000000. 3523 16S rRNA gene accession number: Y11374. 3524 Description of Apilactobacillus apinorum comb. nov. 3525 Apilactobacillus apinorum (a.pi.no’rum. N.L. gen. pl. n. apinorum of the Apini, referring to the isolation 3526 of this species from several species of honey bees). 3527 Basonym: Lactobacillus apinorum Olofsson et al. 2014, 3113VP 3528 Growth is observed at anaerobic conditions in the range of 15 – 50°C and pH 3.0 ‐ 12.0 [89]. The 3529 genome size of the type strain is 1.36 Mbp. The mol% GC content of DNA is 34.9. 3530 Isolated from honey stomach of the honeybee. 3531 The type strain is Fhon13NT = DSM 26257T = CCUG 63287T. 3532 Genome sequence accession number: JXCT00000000. 3533 16S rRNA gene accession number: JX099541.

93

3534 Description of Apilactobacillus kosoi comb. nov. 3535 Apilactobacillus kosoi (ko’so.i. N.L. gen. n. kosoi, of kôso, a high sucrose fermented beverage in Japan, 3536 the origin of the type strain). 3537 Basonym: Lactobacillus kosoi Chiou et al., 2018, 2707VL 3538 The species is described in [322, 323]. A. kosoi is most closely related to A. micheneri; major 3539 physiological properties are shared with A. micheneri, A. timberlakei and A. quenuiae. The genome 3540 size of the type strain is 1.42 Mbp. The mol% GC content of DNA is 30.5. 3541 Isolated from koso, a Japanese sugar‐vegetable fermented beverage. 3542 The type strain is 10HT = NBRC 113063T = BCRC 81100T. 3543 Genome sequence accession number: BEXE01000000. 3544 16S rRNA gene accession number: LC318484 3545 Description of Apilactobacillus micheneri comb. nov. 3546 Apilactobacillus micheneri (mi.che’ne.ri. N.L. gen. masc. n. micheneri named in honor of Charles D. 3547 Michener‘s contributions to the study of bees in natural habitats). 3548 Basonym: Lactobacillus micheneri McFrederick et al. 2018, 1993VP 3549 Major physiological properties are shared with A. timberlakei and A. quenuiae [324]. The genome size 3550 of the type strain is 1.46 Mbp. The mol% GC content of DNA is 30.3. 3551 Isolated from bees and flowers. 3552 The type strain is Hlig3T = DSM 104126T = NRRL B‐65473T. 3553 Genome sequence accession number: POSO00000000. 3554 16S rRNA gene accession number: KT833121. 3555 Description of Apilactobacillus ozensis comb. nov. 3556 Apilactobacillus ozensis (o.zen’sis. N.L. masc. adj. ozensis of Oze, the Japanese National Park from 3557 where the type strain was isolated). 3558 Basonym: Lactobacillus ozensis Kawasaki et al. 2011, 2437VP 3559 A. ozensis grows anaerobically but not aerobically; growth is inhibited by 1.5% NaCl [325]. The genome 3560 size of the type strain is 1.48 Mbp. The mol% GC content of DNA is 31.9. 3561 Isolated from a chrysanthemum flower. 3562 The type strain is Mizu2‐1T = DSM 23829T = JCM 17196T. 3563 Genome sequence accession number: AYYQ00000000. 3564 16S rRNA gene accession number: AB572588. 3565 Description of Apilactobacillus quenuiae comb. nov. 3566 Apilactobacillus quenuiae (que.nu’i.ae. N.L. gen. fem. n. quenuiae, named in recognition of Cécile 3567 Plateaux‐Quénu’s contributions to the biology of bees). 3568 Basonym: Lactobacillus quenuiae Frederick et al. 2018, 1884VP 3569 A description of the speices is provided in [324]. The genome size of the type strain is 1.58 Mbp. The 3570 mol% GC content of DNA is 30.3.

94

3571 Isolated as part of the core microbiome of wild bees and from flowers. 3572 The type strain is HV_6T = DSM 104127T = NRRL B‐65474T. 3573 Genome sequence accession number: POSN00000000. 3574 16S rRNA gene accession number: KX656667. 3575 Description of Apilactobacillus timberlakei comb. nov. 3576 Apilactobacillus timberlakei (tim.ber.lake’i. N.L. gen. masc. n. timberlakei names in honor of Philip 3577 Timberlake’s work on bee taxonomy). 3578 Basonym: Lactobacillus timberlakei McFrederick et al. 2018, 1884VP 3579 Aerotolerant [324]; the genome size of the type strain is 1.54 Mbp. The mol% GC content of DNA is 3580 30.5. 3581 Isolated as part of the core microbiome of wild bees, and from flowers. 3582 The type strain is HV_12T = DSM 104128T = NRRL B‐65472T. 3583 Genome sequence accession number: POST00000000. 3584 16S rRNA gene accession number: KX656650. 3585 DESCRIPTION OF LENTILACTOBACILLUS GEN. NOV. 3586 Lentilactobacillus (Len.ti.lac.to.ba.cil’lus. L. masc. adj. lentus slow, sluggish, referring to the slow 3587 growth of species in the genus with lactate or propanediol as carbon course; N.L. masc. n. Lactobacillus 3588 a bacterial genus name; N.L. masc. n. Lentilactobacillus a slow [growing] lactobacillus). 3589 Gram‐positive, rod‐shaped, catalase negative, heterofermentative. Most strains grow at 15°C and 3590 some also grow at 45°C, the pH range of growth is highly variable but optimal growth is typically 3591 observed below pH 6.0. The genome size ranges from 1.57 Mbp for Lentilactobacillus senioris to 4.91 3592 Mbp for Lentilactobacillus parakefiri, the mol% GC content of DNA ranges from 39.1 – 45.2%. Strains 3593 in the genus were isolated from silage, fermented vegetables, particularly as secondary fermentation 3594 or spoilage microbiota, (spoiled) wine and cereal mashes. Generally, strains in the species lead a free‐ 3595 living lifestyle; individual species of the genus, particularly L. senioris, appear to transition to a 3596 specialized, host adapted lifestyle. Lentilactobacillus species generally metabolize a broad spectrum 3597 of pentoses, hexoses, and disaccharides. Most species metabolize lactate to 1,2‐propanediol and / or 3598 1,2‐propanediol to propanol and propionate; these pathways are virtually exclusive to 3599 heterofermentative lactobacilli and, among these, most common and most frequent in 3600 Lentilactobacillus. Most Lentilactobacillus species also convert agmatine, a product of bacterial 3601 decarboxylation of arginine, via the agmatine deiminase pathway [14, 326]; in lactobacilli, this 3602 pathway is associated with a free‐living lifestyle. Lentilactobacillus species are used commercially as 3603 silage starter cultures, and in few dairy and cereal applications. 3604 A phylogenetic tree on the basis of 16S rRNA genes of all species in the genus Lentilactobacillus is 3605 provided in Figure S6S. 3606 The type species of the genus is Lentilactobacillus buchneri comb. nov.; Lentilactobacillus was 3607 previously referred to as L. buchneri group. 3608 Description of Lentilactobacillus buchneri comb. nov. 3609 Lentilactobacillus buchneri (buch’ne.ri. N.L. gen. n. buchneri of Buchner, referring to the German 3610 microbiologist Buchner).

95

3611 Basonym: (Bacillus buchneri [sic] Henneberg 1903, 163) Bergey et al. 1923, 251 3612 (Approved Lists) 3613 Biochemical characteristics of L. buchneri were described as being similar to L. brevis [11, 231] but L. 3614 buchneri differs with regards to the production of 1,2 propanediol from lactate. The genome size of 3615 the type strain is 2.45 Mbp. The mol% GC content of DNA is 44.4. 3616 Isolated from pressed yeast, milk, cheese, fermenting plant material and the human mouth. L. 3617 buchneri is used commercially as silage inoculant. 3618 The type strain is ATCC 4005T = CCUG 21532T = CIP 103023T =DSM 20057T = JCM 1115T = LMG 6892T = 3619 NCAIM B.01145T = NRRL B‐1837T = VKM B‐1599T. 3620 Genome sequence accession number: AZDM00000000. 3621 16S rRNA gene accession number: AB205055. 3622 Description of Lentilactobacillus curieae comb. nov. 3623 Lentilactobacillus curieae (cu.rie’ae. N.L. fem. gen. n. curieae of Curie, named after Marie Curie, to 3624 acknowledge a role model for women in science). 3625 Basonym: Lactobacillus curieae Lei et al. 2013, 2504VP 3626 Description: Growth is observed at 15 and 45°C and up to 8% NaCl [327]. The genome size of the type 3627 strain is 2.10 Mbp. The mol% GC content of DNA is 39.8. 3628 Isolated from a stinky tofu brine, cocoa bean fermentations and from cheese curd powder. 3629 The type strain is CCTCC M 2011381T = S1L19T = JCM 18524T. 3630 Genome sequence accession number: CP018906. 3631 16S rRNA gene accession number: JQ086550. 3632 Description of Lentilactobacillus diolivorans comb. nov. 3633 Lentilactobacillus diolivorans (di.o.li.vo’rans. N.L. n. diol from 1,2‐propanediol; L. pres. part. vorans 3634 eating; N.L. part. adj. diolivorans eating diols). 3635 Basonym: Lactobacillus diolivorans Kroonemen et al. 2001, 645VP 3636 Growth is observed between 20 and 40°C, and between pH 3.8 and 7. L. diolivorans was the first lactic 3637 acid bacterium for which the metabolic pathway for propanediol and metabolism to propanol 3638 and propionate or 1,3 propanediol and 3‐hydroxypropionate, respectively, was thoroughly described 3639 [328]. This metabolic pathway is functional is multiple other lactobacilli [14, 18]. The genome size of 3640 the type strain is 3.27 Mbp. The mol% GC content of DNA is 40.0. 3641 Isolated from maize silage and as a spoilage organism in vegetable (cucumber) fermentations and 3642 fermented dairy products. 3643 The type strain is JKD6T = DSM 14421T = JCM 12183T = LMG 19667T. 3644 Genome sequence accession number: AZEY00000000. 3645 16S rRNA gene accession number: AF264701. 3646 Description of Lentilactobacillus farraginis comb. nov. 3647 Lentilactobacillus farraginis (far.ra’gi.nis. L. gen. n. farraginis of mash, referring to soshu mash as an 3648 ingredient of the compost from which the type strain was isolated).

96

3649 Basonym: Lactobacillus farraginis Endo and Okada 2007, 711VP 3650 Description: Growth is observed at 15 and 45°C and up to pH 9.0 for some strains [329]. The genome 3651 size of the type strain is 2.86 Mbp. The mol% GC content of DNA is 42.1. 3652 Isolated from isolated from a compost of distilled shochu residue. 3653 The type strain is DSM 18382T = JCM 14108T = NRIC 0676T. 3654 Genome sequence accession number: AZFY00000000. 3655 16S rRNA gene accession number: AB262731. 3656 Description of Lentilactobacillus hilgardii comb. nov. 3657 Lentilactobacillus hilgardii (hil.gar’di.i. N.L. gen. n. hilgardii of Hilgard, named after E.W.Hilgard, a 3658 pioneer of enology in the State of California, U.S.A). 3659 Basonym: Douglas and Cruess 1936, 115 (Approved Lists); the species was 3660 initially described in 1936; the description was emended in 1949 after the original type strain was lost 3661 [330, 331] 3662 Strains grow optimally between pH 4.5 and 5.5 and in the range of 15 to 40°C [330, 331]. The genome 3663 size of the type strain is 2.60 Mbp. The mol% GC content of DNA is 39.6. 3664 Isolated from spoiled wine, kefir grains, mezcal fermentations and silage. 3665 The type strain is 9T = ATCC 8290T = CIP 103007T = DSM 20176T = JCM 1155T = LMG 6895T. 3666 Genome sequence accession number: AZDF00000000. 3667 16S rRNA gene accession number: M58821. 3668 Description of Lentilactobacillus kefiri comb. nov. 3669 Lentilactobacillus kefiri (ke.fi’ri. N.L. gen. n. kefiri, of kefir, referring to the source of isolation). 3670 Basonym: Lactobacillus kefir Kandler and Kunath 1983, 672VL 3671 Characteristics are described in [332]. Growth is observed at 15 but not at 45 °C; the genome size of 3672 the type strain is 2.23 Mbp. The mol% GC content of DNA is 41.7. 3673 Isolated from kefir as part of the core microbiota. 3674 The type strain is A/KT = ATCC 35411T= CIP 103006T = DSM 20587T = JCM 5818T = LMG 9480T. 3675 Genome sequence accession number: AYYV00000000. 3676 16S rRNA gene accession number: AJ621553. 3677 Description of Lentilactobacillus kisonensis comb. nov. 3678 Lentilactobacillus kisonensis (ki.so.nen’sis. N.L. masc. adj. kisonensis from Kiso, the county in Japan, 3679 from where the type strain was isolated). 3680 Basonym: Lactobacillus kisonensis Watanabe et al. 2009, 757VP 3681 Description. Growth is observed at 10 but not at 45 °C and between pH 4.5 to 8.0 [333]. The genome 3682 size of the type strain is 3.01 Mbp. The mol% GC content of DNA is 41.7. 3683 Isolated from a pickle brine. 3684 The type strain is YIT 11168T = DSM 19906T = JCM 15041T = NRIC 074T.

97

3685 Genome sequence accession number: AZEB00000000. 3686 16S rRNA gene accession number: AB366388. 3687 Description of Lentilactobacillus otakiensis comb. nov. 3688 Lentilactobacillus otakiensis (o.ta.ki.en’sis. N.L. masc. adj. otakiensis from Otaki, the village in Japan, 3689 from where the type strain was isolated). 3690 Basonym: Lactobacillus otakiensis Watanabe et al. 2009, 758VP 3691 Physiological characteristics and origin are similar to L. kisonensis [333]. The genome size of the type 3692 strain is 2.35 Mbp. The mol% GC content of DNA is 42.4. 3693 Isolated from sunki, a fermented turnip product and from kefir. 3694 The type strain is YIT 11163T = DSM 19908T = JCM 15040T= NRIC 0742T. 3695 Genome sequence accession number: AZED00000000. 3696 16S rRNA gene accession number: AB366386. 3697 Description of Lentilactobacillus parabuchneri comb. nov. 3698 Lentilactobacillus (Gr. pref. para beside; N.L. gen. n. buchneri a species epithet; N.L. gen. n. 3699 parabuchneri beside L. buchneri, referring to the close relationship with this organism). 3700 Basonym: Lactobacillus parabuchneri Farrow et al. 1988, 371VL; strains of the species were previously 3701 classified as L. ferintoshensis [334] or L. frigidus [64, 335] 3702 Characteristics are described in [278]; growth is observed at 10 and 40°C. The genome size of the type 3703 strain is 2.61 Mbp. The mol% GC content of DNA is 43.5. 3704 Isolated from dairy products, saliva, silage, spoiled beer, and some strains were shown to persist over 3705 month in whiskey mashes in Scottish distilleries [334]. 3706 The type strain is 6ET = ATCC 49374T= DSM 5707T = JCM 12493T = LMG 11457T. 3707 Genome sequence accession number: AZGK00000000. 3708 16S rRNA gene accession number: AB205056. 3709 Description of Lentilactobacillus parafarraginis comb. nov. 3710 Lentilactobacillus parafarraginis (Gr. pref. para beside; L. gen. n. farraginis a species epithet; N.L. gen. 3711 n. parafarraginis beside L. farraginis, referring to the close relationship with this organism). 3712 Basonym: Lactobacillus parafarraginis Endo and Okada 2007, 711VP 3713 Physiological characteristics are similar to L. farraginis but growth is observed only between 20 and 3714 37°C [329]. The genome size of the type strain is 3.08 Mbp. The mol% GC content of DNA is 45.2. 3715 Isolated from a compost of distilled shochu residue, silage, fermented vegetables, and kefir grains. 3716 The type strain is NRIC 0676T = DSM 18390T = JCM 14109T = NRIC 0677T. 3717 Genome sequence accession number: AZFZ00000000. 3718 16S rRNA gene accession number: AB262734. 3719 Description of Lentilactobacillus parakefiri comb. nov. 3720 Lentilactobacillus parakefiri (pa.ra.ke'fir.i. Gr. pref. para beside; N.L. gen. n. kefiri a species epithet; 3721 N.L. masc. adj. parakefiri beside L. kefiri, referring to the close relationship with this organism).

98

3722 Basonym: Takizawa et al. 1994, 438VP. The classification of L. parakefiri as 3723 separate species was disputed as the first published genome sequence of the type strain was virtually 3724 identical to L. kefiri [14, 16] but re‐sequencing of the type strain supported classification of L. parakefiri 3725 as separate species [336] 3726 Growth is observed at 15 but not at 45°C [101]. The genome size of the type strain is 4.91 Mbp. The 3727 mol% GC content of DNA is 42.6. 3728 Isolated from kefir grains. 3729 The type strain is GCL 1731T = ATCC 51648T= CCUG 39468T = CIP 104242T = DSM 10551T = LMG 15133T. 3730 Genome sequence accession number: AZEN00000000. 3731 16S rRNA gene accession number: AY026750. 3732 Description of Lentilactobacillus raoultii sp. nov. 3733 Lentilactobacillus raoultii (ra.oul’ti.i. N.L. gen. n. raoultii of Raoult, named after the microbiologist 3734 Didier Raoult). 3735 The species was effectively but not validly published as Lactobacillus raoultii Nicaise et al. 2019 [337]. 3736 Growth is observed between 25 – 45°C and between pH 5 and 7.5; the genome size of the type strain 3737 is 3.07 Mbp. The mol% GC content of DNA is 41.4. 3738 Isolated from the vagina of a healthy women. 3739 The type strain is Strain Marseille P4006T = CSUR P4006T = LMG 31598T = CCUG 71848T. 3740 Genome sequence accession number: OVSN00000000. 3741 16S rRNA gene accession number: LT854294. 3742 Description of Lentilactobacillus rapi comb. nov. 3743 Lentilactobacillus rapi (ra’pi. L. gen. n. rapi of a turnip, the substrate for fermented sunki products). 3744 Basonym: Lactobacillus rapi Watanabe et al. 2009, 759VP 3745 Origin and physiological properties are similar to L. kisonensis [333]. The genome size of the type strain 3746 is 2.86 Mbp. The mol% GC content of DNA is 43.0. 3747 Isolated from sunki and other vegetable fermentations. 3748 The type strain is YIT 11204T = DSM 19907T = JCM 15042T = NRIC 0743T. 3749 Genome sequence accession number: AZEI00000000. 3750 16S rRNA gene accession number: AB366389. 3751 Description of Lentilactobacillus senioris comb. nov. 3752 Lentilactobacillus senioris (se.ni.o’ris. L. gen. n. senioris of an elderly person, indicating the source of 3753 the type strain). 3754 Basonym: Lactobacillus senioris Oki et al., 2012, 606VP 3755 Growth is observed at 15 and 37 °C but not at 45°C; the type strain was isolated from human feces 3756 [173]. L. senioris is the most distantly related member of the genus, has the smallest genome size (1.57 3757 Mbp) and lowest GC content (39.9) among species in the genus, and does not share the signature 3758 genes that are shared by other lentilactobacilli, which may indicate that L. senioris transitions from a 3759 free‐living to a host‐adapted lifestyle.

99

3760 Isolated from from the faeces of a 100‐year‐old female. 3761 The type strain is YIT 12364T = DSM 24302T = JCM 17472T. 3762 Genome sequence accession number: AYZR00000000. 3763 16S rRNA gene accession number: AB602570. 3764 Description of Lentilactobacillus sunkii comb. nov. 3765 Lentilactobacillus sunkii (sun’ki.i. N.L. gen. n. sunkii of sunki, non‐salted Japanese traditional pickle). 3766 Basonym: Lactobacillus sunkii Watanabe et al. 2009, 759VP 3767 Physiological properties and origin are comparable to L. kisonensis [333]. The genome size of the type 3768 strain is 2.69 Mbp. The mol% GC content of DNA is 42.1. 3769 Isolated from sunki, a fermented turnip product, and from kefir. 3770 The type strain is YIT 11161T = DSM 19904T = JCM 15039T = NRIC 0744T. 3771 Genome sequence accession number: AZEA00000000. 3772 16S rRNA gene accession number: AB366385. 3773 NOTE ADDED IN PROOF 3774 Species that were added at the proof stage: 3775 Description of Lapidilactobacillus achengensis comb. nov. 3776 Lapidilactobacillus achengensis (a.cheng.en´sis. N.L. masc. adj. achengensis, pertaining to Acheng, a 3777 county in Heilongjiang Province, P.R. China). 3778 Basonym: Lactobacillus achengensis Long et al. 2020, 15VP. 3779 L. achengensis grows between 10 and 37°C but not at 5 and 45°C and metabolises several pentoses 3780 and a broad spectrum of disaccharides [338]. The genome size of the type strain is 2.64 Mbp. The 3781 mol% GC content of DNA is 49.0. 3782 Isolated from a vegetable fermentation [338]. 3783 The type strain is 247‐4T = NCIMB 15155T = CCM 8897T = LMG 31059T = CCTCC AB 2018410T. 3784 Genome sequence accession number: RHOV00000000. 3785 16S rRNA gene accession number: MK110810. 3786 Description of Lapidilactobacillus gannanensis comb. nov. 3787 Lapidilactobacillus gannanensis (gan.nan.en´sis. N.L. masc. adj. gannanensis, pertaining to Gannan, a 3788 county in Heilongjiang Province, P.R. China). 3789 Basonym: Lactobacillus gannanensis Long et al. 2020, 16VP. 3790 L. gannanensis grows between 15 and 37°C but not at 10 and 45°C; the strain produces acid from D‐ 3791 glucose, N‐acetylglucosamine, salicin, cellobiose and gentiobiose but not from pentoses [338]. The 3792 genome size of the type strain is 2.39 Mbp. The mol% GC content of DNA is 40.8. 3793 Isolated from a vegetable fermentation [338]. 3794 The type strain is 143‐1T = NCIMB 15157T = CCM 8937T = CCTCC AB 2018409T. 3795 Genome sequence accession number: RHOT00000000.

100

3796 16S rRNA gene accession number: MK110813. 3797 Description of Lapidilactobacillus mulanensis comb. nov. 3798 Lapidilactobacillus mulanensis (mu.lan.en´sis. N.L. masc. adj. mulanensis, pertaining to Mulan, a 3799 county in Heilongjiang Province, P.R. China). 3800 Basonym: Lactobacillus mulanensis Long et al. 2020, 14VP. 3801 L. mulanensis grows between 15 and 32°C; the strain produces acid from hexoses and disaccharides 3802 but not from pentoses [338]. The genome size of the type strain is 2.32 Mbp. The mol% GC content of 3803 DNA is 42.5. 3804 Isolated from a vegetable fermentation [338]. 3805 The type strain is 143‐6T = NCIMB 15162T = CCM 8951T = JCM 33274T = CCTCC AB 2018411T. 3806 Genome sequence accession number: RHOW00000000. 3807 16S rRNA gene accession number: MK110808. 3808 Description of Lapidilactobacillus wuchangensis comb. nov. 3809 Lapidilactobacillus wuchangensis (wu.chang.en´sis. N.L. masc. adj. wuchangensis, pertaining to 3810 Wuchang, a county in Heilongjiang Province, P.R. China). 3811 Basonym: Lactobacillus wuchangensis Long et al. 2020, 15VP. 3812 L. mulanensis grows between 15 and 37°C but not at 10 and 45°C; the strain produces L(+)‐lactate 3813 from D‐ribose, D‐glucose, N‐acetylglucosamine and cellobiose [338]. The genome size of the type 3814 strain is 2.53 Mbp. The mol% GC content of DNA is 41.7. 3815 Isolated from a vegetable fermentation [338]. 3816 The type strain is 17‐4T = NCIMB 15161T = CCM 8946T = JCM 33271T = CCTCC AB 2018406T. 3817 Genome sequence accession number: RHOU00000000. 3818 16S rRNA gene accession number: MK110811. 3819 Description of Lacticaseibacillus daqingensis comb. nov. 3820 Lacticaseibacillus daqingensis (da.qing.en´sis. N.L. masc. adj. daqingensis, pertaining to Daqing, a city 3821 in in Heilongjiang Province, P.R. China). 3822 Basonym: Lactobacillus daqingensis Long et al. 2020, 14VP. 3823 L. daqingensis grows at 10 ‐ 37°C but not at 5° and 45°C [338]. The genome size of the type strain is 3824 2.74 Mbp. The mol% GC content of DNA is 58.0. 3825 Isolated from a vegetable fermentation [338]. 3826 The type strain is 143‐4(a)T = NCIMB 15173T = CCM 8948T = JCM 33273T = CCTCC 2018390T. 3827 Genome sequence accession number: RHOH00000000. 3828 16S rRNA gene accession number: MK110842. 3829 Description of Lacticaseibacillus hegangensis comb. nov. 3830 Lacticaseibacillus hegangensis (he.gang.en´sis. N.L. masc. adj. hegangensis, pertaining to Hegang, a 3831 city in Heilongjiang Province, P.R. China). 3832 Basonym: Lactobacillus hegangensis Long et al. 2020, 12VP.

101

3833 Properties of L. hegangensis are similar to L. daqingensis [338]. The genome size of the type strain is 3834 2.50 Mbp. The mol% GC content of DNA is 55.5. 3835 Isolated from a vegetable fermentation [338]. 3836 The type strain is 73‐4T = NCIMB 15177T = CCM 8912T = CCTCC AB 2018407T. 3837 Genome sequence accession number: RHOL00000000. 3838 16S rRNA gene accession number: MK110833. 3839 Description of Lacticaseibacillus suibinensis comb. nov. 3840 Lacticaseibacillus suibinensis (sui.bin.en´sis. N.L. masc. adj. suibinensis, pertaining to Suibin, a county 3841 in Heilongjiang Province, P.R. China). 3842 Basonym: Lactobacillus suibinensis Long et al. 2020, 12VP. 3843 Properties of L. suibiensis are similar to L. daqingensis but L. suibiensis deaminates arginine [338]. The 3844 genome size of the type strain is 2.56 Mbp. The mol% GC content of DNA is 53.0. 3845 Isolated from a vegetable fermentation [338]. 3846 The type strain is 247‐3T = NCIMB 15176T = JCM 33275T. 3847 Genome sequence accession number: RHOK00000000. 3848 16S rRNA gene accession number: MK110834. 3849 Description of Lacticaseibacillus yichunensis comb. nov. 3850 Lacticaseibacillus yichunensis (yi.chun.en´sis. N.L. masc. adj. yichunensis, pertaining to Yichun, a city in 3851 Heilongjiang Province, P.R. China). 3852 Basonym: Lactobacillus yichunensis Long et al. 2020, 14VP. 3853 Properties of L. yichunensis are similar to L. daqingensis, but it does not grow at 37°C. [338]. The 3854 genome size of the type strain is 2.56 Mbp. The mol% GC content of DNA is 55.4. 3855 Isolated from a vegetable fermentation [338]. 3856 The type strain is 33‐1T = NCIMB 15169T = CCM 8947T = JCM 33272T = CCTCC 2018405T. 3857 Genome sequence accession number: RHOG00000000. 3858 16S rRNA gene accession number: MK110845. 3859 Description of Loigolactobacillus binensis comb. nov. 3860 Loigolactobacillus binensis (bin.en´sis. N.L. masc. adj. binensis, pertaining to Bin, a county in 3861 Heilongjiang Province, P.R. China). 3862 Basonym: Lactobacillus binensis Long et al. 2020, 16VP. 3863 L. binensis grows between 10 and 37°C but not at 5 and 45°C; the strain produces acid from several 3864 hexoses, sugar alcohols and maltose, but not from pentoses [338]. The genome size of the type strain 3865 is 2.85 Mbp. The mol% GC content of DNA is 43.5. 3866 Isolated from a vegetable fermentation [338]. 3867 The type strain is 735‐2T = NCIMB 15190T = CCM 8925T = LMG 31186T. 3868 Genome sequence accession number: BJDN00000000.

102

3869 16S rRNA gene accession number: LC438524. 3870 Description of Lactiplantibacillus garii comb. nov. 3871 Lactiplantibacillus garii (ga’ri.i N.L. gen. n. garii of gari, the fermented cassava product from which the 3872 type strain was isolated). 3873 Basonym: Lactobacillus garii Diaz et al. 2020, 5VP. 3874 L. garii grows in the temperature range of 6 – 42 °C and in the pH range of 4.0 to 8.8. The type strain 3875 produces D(‐)‐lactate from a wide spectrum of pentoses, hexoses, and disaccharides [339]. The 3876 genome size of the type strain is 2.97 Mbp. The mol% GC content of DNA is 48.3. 3877 Isolated from gari, a fermented cassava product [339]. 3878 The type strain is FI11369T = NCIMB 15148T = DSM 108249T. 3879 Genome sequence accession number: QWZQ00000000. 3880 16S rRNA gene accession number: MN81791. 3881 Description of Levilactobacillus angrenensis comb. nov. 3882 Levilactobacillus angrenensis (ang.ren.en´sis. N.L. masc. adj. angrenensis, pertaining to Angren, a 3883 county in the Tibet Autonomous Region, PR China, where the bacterium was isolated). 3884 Basonym: Lactobacillus angrenensis Long et al. 2020, 16VP. 3885 L. angrenensis grows between 10 and 37°C but not at 5 and 45°C [338]. The genome size of the type 3886 strain is 2.80 Mbp. The mol% GC content of DNA is 50.5. 3887 Isolated from a fermented dairy beverage [338]. 3888 The type strain is M1530‐1T = NCIMB 15150T = CCM 8893T = LMG 31046T = CCTCC AB 2018402T. 3889 Genome sequence accession number: RHOB00000000. 3890 16S rRNA gene accession number: MK110858. 3891 Description of Levilactobacillus enshiensis comb. nov. 3892 Levilactobacillus enshiensis (en.shi.en'sis. N.L. masc. adj. enshiensis pertaining to Enshi, the prefecture 3893 in Hubei Province of the P.R. China where strain was isolated). 3894 Basonym: Lactobacillus enshiensis Zhang et al. 2020, 6VP. 3895 L. enshiensis grows in the pH range of 4.0 to 10 and between 20 and 45°C but not at 15 and 50°C [340]. 3896 Acid is produced from a wide spectrum of pentoses, hexoses, disaccharides and several sugar alcohols; 3897 citrate is converted to malate [340]. In silico analyses presented in the species new description suggest 3898 a functional glycolytic pathway, however, phosphofructokinase, a key enzyme of glycolysis that is 3899 absent in virtually all heterofermentative lactobacilli [14] is also absent in the genome of L. enshiensis 3900 and the spectrum of metabolites from glucose demonstrate heterofermentative metabolism [340]. 3901 The genome size of the type strain is 3.07 Mbp. The mol% GC content of DNA is 47.8. 3902 Isolated from Zha‐Chili, a fermented product from mustard greens [340]. 3903 The type strain is HBUAS57009T = GDMCC 1.1664T = KACC 21424T. 3904 Genome sequence accession number: SULH00000000. 3905 16S rRNA gene accession number: MN082021.

103

3906 AUTHOR STATEMENTS 3907 Funding information: Jinshui Zheng acknowledges support from the National Natural Science 3908 Foundation of China (NSFC) (31970003 and 31770003); Stijn Wittouck acknowledges stipend support 3909 from the Fonds voor Wetenschappelijk Onderzoek ‐ Vlaanderen. Michael Gänzle acknowledges 3910 financial support from the Canada Research Chairs Program. Sarah Lebeer acknowledges funding 3911 through from Flanders Innovation and Entrepreneurship (VLAIO) IWT‐SBO project 150052. 3912 Acknowledgements. We are indebted to Aharon Oren (Jerusalem, Israel) for nomenclatural advice. 3913 Ethical statement. The study did not use animals or humans for research. 3914 Conflicts of interest. The authors declare no conflict of interest. Bruno Pot is employed by Yakult 3915 Europe but has no conflict of interest for this paper.

3916 ABBREVIATIONS 3917 AAI, pairwise amino acid identity 3918 cAAI, pairwise amino acid identity of conserved genes 3919 ANI, average nucleotide identity.

3920 REFERENCES 3921 3922 1. Schleifer K‐H (2009) Family V. Leuconostocaceae fam. nov. In: De Vos P, Garrity G, Jones D, 3923 Krieg N, Ludwig W, Rainey F, Schleifer K, Whitman W (eds) Bergey’s Man. Syst. Bacteriol. (The 3924 Firmicutes), vol 3, 2nd ed. Springer, Dordrecht, Heidelberg, London, p 624 3925 2. Orla‐Jensen S (1919) The lactic acid bacteria. Andr Fred Høst and Son, Copenhagen 3926 3. Schleifer KH, Stackebrandt E (1983) Molecular systematics of prokaryotes. Annu Rev Microbiol 3927 Microbiol 37:143–187 3928 4. Chun J, Oren A, Ventosa A, et al (2018) Proposed minimal standards for the use of genome data 3929 for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466 3930 5. Konstantinidis KT, Tiedje JM (2005) Towards a genome‐based taxonomy for prokaryotes. J 3931 Bacteriol 187:6258–6264 3932 6. Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. 3933 Nat Rev Microbiol 6:431–440 3934 7. Richter M, Rosselló‐Móra R (2009) Shifting the genomic gold standard for the prokaryotic 3935 species definition. Proc Natl Acad Sci 106:19126–19131 3936 8. Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average 3937 nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of 3938 prokaryotes. Int J Syst Evol Microbiol 64:346–351 3939 9. Jain C, Rodriguez‐R LM, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI 3940 analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9:5114 3941 10. Wittouck S, Wuyts S, Meehan CJ, van Noort V, Lebeer S (2019) A genome‐based species 3942 taxonomy of the Lactobacillus Genus Complex. mSystems 4:e00264‐19 3943 11. Pot B, Felis G, De Bruyne K, Tsakalidou E, Papadimitriou K, Leisner J, Vandamme P a: biodiversity 3944 and taxonomy., John Wiley & Sons, Inc, Hoboken N (2014) The genus Lactobacillus. In:

104

3945 Holzapfel W, Wood B (eds) Lact. Acid Bact. Biodivers. Taxon. John Wiley & Sons, Inc, Hoboken, 3946 NJ., pp 249–353 3947 12. Hammes WP, Hertel C (2006) The genera Lactobacillus and Carnobacterium. In: The 3948 Prokaryotes. Springer US, New York, NY, pp 320–403 3949 13. Salvetti E, Torriani S, Felis GE (2012) The genus Lactobacillus: A taxonomic update. Probiotics 3950 Antimicrob Proteins 4:217–226 3951 14. Zheng J, Ruan L, Sun M, Gänzle MG (2015) A genomic view of lactobacilli and pediococci 3952 demonstrates that phylogeny matches ecology and physiology. Appl Environ Microbiol 3953 81:7233–7243 3954 15. Salvetti E, Harris HMB, Felis GE, O’Toole PW (2018) Comparative genomics of the genus 3955 Lactobacillus reveals robust phylogroups that provide the basis for reclassification. Appl 3956 Environ Microbiol 84:e00993‐18 3957 16. Sun Z, Harris HMB, McCann A, et al (2015) Expanding the biotechnology potential of lactobacilli 3958 through comparative genomics of 213 strains and associated genera. Nat Commun 6:8322 3959 17. Duar RM, Lin XB, Zheng J, Martino ME, Grenier T, Pérez‐Muñoz ME, Leulier F, Gänzle M, Walter 3960 J (2017) Lifestyles in transition: evolution and natural history of the genus Lactobacillus. FEMS 3961 Microbiol Rev 41:S27–S48 3962 18. Gänzle MG (2015) Lactic metabolism revisited: Metabolism of lactic acid bacteria in food 3963 fermentations and food spoilage. Curr Opin Food Sci 2:106–117 3964 19. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a 3965 consensus approach to bacterial systematics. Microbiol Rev 60:407–438 3966 20. Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069 3967 21. Hyatt D, Chen G‐L, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic 3968 gene recognition and translation initiation site identification. BMC Bioinformatics 11:119 3969 22. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) 3970 BLAST+: architecture and applications. BMC Bioinformatics 10:421 3971 23. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high 3972 throughput. Nucleic Acids Res 32:1792–1797 3973 24. Capella‐Gutiérrez S, Silla‐Martínez JM, Gabaldón T (2009) trimAl: a tool for automated 3974 alignment trimming in large‐scale phylogenetic analyses. Bioinformatics 25:1972–1973 3975 25. Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post‐analysis of large 3976 phylogenies. Bioinformatics 30:1312–1313 3977 26. Letunic I, Bork P (2019) Interactive Tree Of Life (iTOL) v4: Recent updates and new 3978 developments. Nucleic Acids Res 47:W256–W259 3979 27. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P‐A, Hugenholtz P 3980 (2018) A standardized bacterial taxonomy based on genome phylogeny substantially revises 3981 the tree of life. Nat Biotechnol 36:996–1004 3982 28. Wittouck S GitHub ‐ SWittouck/progenomics: A toolkit for prokaryotic comparative genomics. 3983 https://github.com/SWittouck/progenomics. Accessed 10 Sep 2019 3984 29. Katoh K, Standley DM (2013) MAFFT Multiple Sequence Alignment Software Version 7: 3985 Improvements in Performance and Usability. Mol Biol Evol 30:772–780 3986 30. Nguyen L‐T, Schmidt HA, von Haeseler A, Minh BQ (2015) IQ‐TREE: A fast and effective 3987 stochastic algorithm for estimating maximum‐likelihood phylogenies. Mol Biol Evol 32:268–

105

3988 274 3989 31. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS (2018) UFBoot2: Improving the 3990 ultrafast bootstrap approximation. Mol Biol Evol 35:518–522 3991 32. Yu G, Smith DK, Zhu H, Guan Y, Lam TT‐Y (2017) GGTREE An R package for visualization and 3992 annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol 3993 Evol 8:28–36 3994 33. Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat 3995 Methods 12:59–60 3996 34. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial 3997 innovation. Nature 405:299–304 3998 35. Kloesges T, Popa O, Martin W, Dagan T (2011) Networks of gene sharing among 329 3999 proteobacterial genomes reveal differences in lateral gene transfer frequency at different 4000 phylogenetic depths. Mol Biol Evol 28:1057–1074 4001 36. Novichkov PS, Omelchenko M V, Gelfand MS, Mironov AA, Wolf YI, Koonin E V (2004) Genome‐ 4002 wide molecular clock and horizontal gene transfer in bacterial evolution. J Bacteriol 186:6575– 4003 6585 4004 37. Emms DM, Kelly S (2015) OrthoFinder: Solving fundamental biases in whole genome 4005 comparisons dramatically improves orthogroup inference accuracy. Genome Biol 16:157 4006 38. Mirdita M, Steinegger M, Söding J (2019) MMseqs2 desktop and local web server app for fast, 4007 interactive sequence searches. Bioinformatics 35:2856–2858 4008 39. GitHub ‐ SWittouck/tidygenomes: Functions to import and process orthogroup data in a tidy 4009 way. https://github.com/SWittouck/tidygenomes. Accessed 10 Sep 2019 4010 40. Wittouck S (2019) Genus‐level taxonomy of lactobacilli. 4011 https://github.com/SWittouck/lacto_genera. 4012 41. Yu Y, Li X, Zhang J, Chai L‐J, Lu Z‐M, Xu Z‐H (2020) Lactobacillus jinshani sp. nov., isolated from 4013 solid‐state vinegar culture of Zhenjiang aromatic vinegar. Antonie Van Leeuwenhoek 113:43– 4014 54 4015 42. Praet J, Meeus I, Cnockaert M, Houf K, Smagghe G, Vandamme P (2015) Novel lactic acid 4016 bacteria isolated from the bumble bee gut: Convivina intestini gen. nov., sp. nov., Lactobacillus 4017 bombicola sp. nov., and Weissella bombi sp. nov. Antonie Van Leeuwenhoek 107:1337–1349 4018 43. Wittouck S, Wuyts S, Lebeer S (2019) Towards a genome‐based reclassification of the genus 4019 Lactobacillus. Appl Environ Microbiol 85:e02155‐18 4020 44. Euzéby J (2010) List of new names and new combinations previouslyeffectively, but not validly, 4021 published. Int J Syst Evol Microbiol 60:469–472 4022 45. Zhang S, Oh J‐H, Alexander LM, Özçam M, van Pijkeren J‐P (2018) d‐Alanyl‐d‐alanine ligase as 4023 a broad‐host‐range counterselection marker in vancomycin‐resistant lactic acid bacteria. J 4024 Bacteriol 200:e00607‐17 4025 46. Vent DH, Indian S, Zhao S, et al (2014) Prodigal: prokaryotic gene recognition and translation 4026 initiation site identification. Nat Commun 6:1–8 4027 47. Wuyts S, Wittouck S, De Boeck I, Allonsius CN, Pasolli E, Segata N, Lebeer S (2017) Large‐scale 4028 phylogenomics of the Lactobacillus casei group highlights taxonomic inconsistencies and 4029 reveals novel clade‐associated features. mSystems 2:e00061‐17 4030 48. Harris HMB, Bourin MJB, Claesson MJ, O’Toole PW (2017) Phylogenomics and comparative

106

4031 genomics of Lactobacillus salivarius, a mammalian gut commensal. Microb genomics 4032 3:e000115 4033 49. Rosselló‐Móra R, Amann R (2015) Past and future species definitions for Bacteria and Archaea. 4034 Syst Appl Microbiol 38:209–216 4035 50. Wieme A, Cleenwerck I, Van Landschoot A, Vandamme P (2012) Pediococcus lolii DSM 19927T 4036 and JCM 15055T are strains of . Int J Syst Evol Microbiol 62:3105–3108 4037 51. Fujisawa T, Shirasaka S, Watabe J, Mitsuoka T (1984) Lactobacillus aviarius sp. nov.: A new 4038 species isolated from the intestine of chickens. Syst Appl Microbiol 5:414–420 4039 52. Martinson VG, Danforth BN, Minckley RL, Rueppell O, Tingek S, Moran NA (2011) A simple and 4040 distinctive microbiota associated with honey bees and bumble bees. Mol Ecol 20:619–628 4041 53. van der Veer C, Hertzberger RY, Bruisten SM, et al (2019) Comparative genomics of human 4042 Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: 4043 implications for in vivo dominance of the vaginal microbiota. Microbiome 7:49 4044 54. Wang W, Hu H, Zijlstra RT, Zheng J, Gänzle MG (2019) Metagenomic reconstructions of gut 4045 microbial metabolism in weanling pigs. BMC Microbiome 7:48 4046 55. Lin XB, Wang T, Stothard P, et al (2018) The evolution of ecological facilitation within mixed‐ 4047 species biofilms in the mouse gastrointestinal tract. ISME J 12:2770–2784 4048 56. Tannock GW, Wilson CM, Loach D, Cook GM, Eason J, O’Toole PW, Holtrop G, Lawley B (2012) 4049 Resource partitioning in relation to cohabitation of Lactobacillus species in the mouse 4050 forestomach. ISME J 6:927–938 4051 57. van de Guchte M, Penaud S, Grimaldi C, et al (2006) The complete genome sequence of 4052 Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. PNAS 103:9274– 4053 9279 4054 58. Gänzle MG (2019) Fermented Foods. In: Doyle MP, Diez‐ Gonzalez F, Hill C (eds) Food Microbiol. 4055 Fundam. Front., 5th ed. ASM Press, pp 855–900 4056 59. Hutkins RW (2019) Microbiology and technology of fermented foods, 2nd. IFT Press, Chigaco, 4057 IL 4058 60. Weiss N, Schillinger U, Kandler O (1983) Lactobacillus lactis, Lactobacillus leichmannii and 4059 Lactobacillus bulgaricus, subjective synonyms of Lactobacillus delbrueckii, and description of 4060 Lactobacillus delbrueckii subsp. lactis comb. nov. and Lactobacillus delbrueckii subsp. 4061 bulgaricus comb. nov. Syst Appl Microbiol 552–7 4062 61. Rogosa M, Wiseman RF, Mitchell JA, Disraely MN, A J Beaman AB (1953) Species differentiation 4063 of oral lactobacilli from man including descriptions of Lactobacillus salivarius nov. spec. and 4064 Lactobacillus cellobiosus nov. spec. J Bacteriol 65:681–699. 4065 62. Leichmann G (1896) Uber die im Brennereiprozess bei der Kunsthefe auftretende spontane 4066 Milchsäuregärung. Zentralbl Bakteriol Parasitenk Abt I1:281‐285. 4067 63. Rogosa M, Sharpe E. (1959) An approach to the classification of the lactobacilli. J Appl Bacteriol 4068 22:29–340 4069 64. Rogosa M, Hansen PA (1971) Nomenclatural considerations of certain species of Lactobacillus 4070 Beijerinck: Request for an opinion. Int J Syst Bacteriol 21:177–186 4071 65. Henneberg W (1903) Zur Kentniss der Milchsäurebakterien der Brennereimaische, der Milch, 4072 des Bieres, der Preßhefe, der Melasse, des Sauerkohls, der sauren Gurken und des Sauerteigs, 4073 sowie einige über die Milchsäurebakterien des menschlichen Magens. Spiritusindustrie 4074 26:329–332

107

4075 66. Dellaglio F, Felis GE, Castioni A, Torriani S, Germond JE (2005) Lactobacillus delbrueckii subsp. 4076 indicus subsp. nov., isolated from Indian dairy products. Int J Syst Evol Microbiol 55:401–404 4077 67. Adimpong DB, Nielsen DS, Sørensen KI, Vogensen FK, Sawadogo‐Lingani H, Derkx PMF, 4078 Jespersen L (2013) Lactobacillus delbrueckii subsp. jakobsenii subsp. nov., isolated from dolo 4079 wort, an alcoholic fermented beverage in Burkina Faso. Int J Syst Evol Microbiol 63:3720–3726 4080 68. Kudo Y, Oki K, Watanabe K (2012) Lactobacillus delbrueckii subsp. sunkii subsp. nov., isolated 4081 from sunki, a traditional Japanese pickle. Int J Syst Evol Microbiol 62:2643–2649 4082 69. Entani E, Masai H, Suzuki K‐I (2009) Lactobacillus acetotolerans, a new species from fermented 4083 vinegar broth. Int J Syst Bacteriol 36:544–549 4084 70. Moro E (1900) Über den Bacillus acidophilus n. sp. Jahrb fur Kinderheilkd und Phys Erziehung 4085 52:38‐55. 4086 71. Hansen PA, Mocquot G (1970) Lactobacillus acidophilus (Moro) comb. nov. Int J Syst 4087 Bacteriolocy 20:325–327 4088 72. Johnson JL, Phelps CF, Cummins CS, London J, Gasser F (1980) Taxonomy of the Lactobacillus 4089 acidophilus group. Int J Syst Bacteriol 30:53–68 4090 73. Bohak I, Back W, Richter L, Ehrmann M, Ludwig W, Schleifer K (1998) Lactobacillus amylolyticus 4091 sp. nov., Isolated from beer malt and beer wort. Syst Appl Microbiol 21:360–364 4092 74. Jakava‐Viljanen M, Murros A, Palva A, Björkroth KJ (2008) Lactobacillus sobrius Konstantinov 4093 et al. 2006 is a later synonym of Lactobacillus amylovorus Nakamura 1981. Int J Syst Evol 4094 Microbiol 58:910–913 4095 75. Nakamura LK (1981) Lactobacillus amylovorus, a new starch‐hydrolyzing species from cattle 4096 waste‐corn fermentations. Int J Syst Bacteriol 31:56–63 4097 76. Leser TTD, Amenuvor JZJ, Jensen TTK, Lindecrona RRH, Boye M, Møller K (2002) Culture‐ 4098 independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl 4099 Environ Microbiol 68:673–690 4100 77. Killer J, Dubná S, Sedláček I, Švec P (2014) Lactobacillus apis sp. nov., from the stomach of 4101 honeybees (Apis mellifera), having an in vitro inhibitory effect on the causative agents of 4102 American and European foulbrood. Int J Syst Evol Microbiol 64:152–157 4103 78. Zhang MZ, Yang M, Su H, Rollins D, Zhang S (2017) Lactobacillus colini sp. nov., isolated from 4104 Northern Bobwhite (Colinus virginianus). Int J Syst Evol Microbiol 67:325–329 4105 79. Brygoo E, Aladame N (1953) Etude d’une espèce nouvelle anaerobic stricte du genre 4106 : E. crispatum n. sp. Ann Inst Pasteur Paris 84:640–651 4107 80. Moore W, Holdeman L (1970) , Arachnia, Actinomyces, Lactobacillus and 4108 Bifidobacterium., 2nd ed. Outline of Clinical Methods in Anaerobic Bacteriology, Blacksburg, 4109 VA: Virginia Polytechnic Institute, Anaerobe Laboratory, 4110 81. Cato EP, Moore WEC, Johnson JL (1983) Synonymy of strains of “Lactobacillus acidophilus” 4111 group A2 (Johnson et al. 1980) with the type strain of Lactobacillus crispatus (Brygoo and 4112 Aladame 1953) Moore and Holdeman 1970. Int J Syst Bacteriol 33:426–428 4113 82. Morita H, Shimazu M, Shiono H, et al (2010) Lactobacillus equicursoris sp. nov., isolated from 4114 the faeces of a thoroughbred racehorse. Int J Syst Evol Microbiol 60:109–112 4115 83. Dicks L, Silvester M, Lawson PA, Collins MD (2000) Lactobacillus fornicalis sp. nov., isolated 4116 from the posterior fornix of the human vagina. Int J Syst Evol Microbiol 50:1253–1258 4117 84. Fujisawa T, Benno Y, Yaeshima T, Mitsuoka T (1992) Taxonomic study of the Lactobacillus

108

4118 acidophilus group, with recognition of Lactobacillus gallinarum sp. nov. and Lactobacillus 4119 johnsonii sp. nov. and synonymy of Lactobacillus acidophilus group A3 (Johnson et al. 1980) 4120 with the type strain of Lactobacillus amylovorus (Nakamura 1981). Int J Syst Bacteriol 42:487– 4121 491 4122 85. Lauer E, Kandler O (1980) Lactobacillus gasseri sp. nov., a new species of the subgenus 4123 Thermobacterium. Zentralbl Bakteriol Parasitenkd Infekt Hyg I Abt Orig C 1:75–78 4124 86. Lauer E, Kandler O (1980) Validation of the publication of new names and new combinations 4125 previously effectively published outside the IJSB List No. 4. Int J Syst Bacteriol 30:601 4126 87. Cousin S, Gulat‐Okalla ML, Motreff L, Gouyette C, Bouchier C, Clermont D, Bizet C (2012) 4127 Lactobacillus gigeriorum sp. nov., isolated from chicken crop. Int J Syst Evol Microbiol 62:330– 4128 334 4129 88. Mitsuoka T, Fujisawa T (1987) Lactobacillus hamsteri, a new species from the intestine of 4130 hamsters. Proc Japan Acad Ser B Phys Biol Sci 63:269–272 4131 89. Olofsson TC, Alsterfjord M, Nilson B, Butler È, Vásquez A (2014) Lactobacillus apinorum sp. 4132 nov., Lactobacillus mellifer sp. nov., Lactobacillus mellis sp. nov., Lactobacillus melliventris sp. 4133 nov., Lactobacillus kimbladii sp. nov., Lactobacillus helsingborgensis sp. nov. and Lactobacillus 4134 kullabergensis sp. nov., isolated from the honey stomach of the honeybee Apis mellifera. Int J 4135 Syst Evol Microbiol 64:3109–3119 4136 90. Bergey D, Harrison F, Breed R, Hammer B, Huntoon F (1925) Bergey’s Manual of Determinative 4137 Bacteriology. In: Bergey D, Harrison F, Breed R, Hammer B, Huntoon F (eds) Bergey’s Man. 4138 Determ. Bacteriol., 2nd ed. The Williams & Wilkins Co, Baltimore, p 462 4139 91. Naser SM, Hagen KE, Vancanneyt M, Cleenwerck I, Swings J, Tompkins TA (2006) Lactobacillus 4140 suntoryeus Cachat and Priest 2005 is a later synonym of Lactobacillus helveticus (Orla‐Jensen 4141 1919) Bergey et al. 1925 (Approved Lists 1980). Int J Syst Evol Microbiol 56:355–60 4142 92. Hammons S, Oh PL, Martínez I, Clark K, Schlegel VL, Sitorius E, Scheideler SE, Walter J (2010) A 4143 small variation in diet influences the Lactobacillus strain composition in the crop of broiler 4144 chickens. Syst Appl Microbiol 33:275–281 4145 93. Cousin S, Motreff L, Gulat‐Okalla M‐L, Gouyette C, Sproer C, Schumann P, Begaud E, Bouchier 4146 C, Clermont D, Bizet C (2013) Lactobacillus pasteurii sp. nov. and Lactobacillus hominis sp. nov. 4147 Int J Syst Evol Microbiol 63:53–59 4148 94. Falsen E, Pascual C, Sjoden B, Ohlen M, Collins MD (1999) Phenotypic and phylogenetic 4149 characterization of a novel Lactobacillus species from human sources: description of 4150 Lactobacillus iners sp. nov. Int J Syst Bacteriol 49:217–221 4151 95. Zeeuwen PL, Boekhorst J, van den Bogaard EH, et al (2012) Microbiome dynamics of human 4152 epidermis following skin barrier disruption. Genome Biol 13:R101 4153 96. Fujisawa T, Itoh K, Benno Y, Mitsuoka T (1990) Lactobacillus intestinalis (ex Hemme 1974) sp. 4154 nov., nom. rev., isolated from the intestines of mice and rats. Int J Syst Bacteriol 40:302–304 4155 97. Gasser F, Mandel M, Rogosa M (1970) Lactobacillus jensenii sp.nov., a new representative of 4156 the subgenus Thermobacterium. J Gen Microbiol 62:219–22 4157 98. Roos S, Engstrand L, Jonsson H (2005) Lactobacillus gastricus sp. nov., Lactobacillus antri sp. 4158 nov., Lactobacillus kalixensis sp. nov. and Lactobacillus ultunensis sp. nov., isolated from 4159 human stomach mucosa. Int J Syst Evol Microbiol 55:77–82 4160 99. Fujisawa T, Adachi S, Toba T, Arihara K, Mitsuoka T (1988) Lactobacillus kefiranofaciens sp. nov. 4161 isolated from kefir grains. Int J Syst Bacteriol 38:12–14

109

4162 100. Vancanneyt M, Mengaud J, Cleenwerck I, Vanhonacker K, Hoste B, Dawyndt P, Degivry MC, 4163 Ringuet D, Janssens D, Swings J (2004) Reclassification of Lactobacillus kefirgranum Takizawa 4164 et al. 1994 as Lactobacillus kefiranofaciens subsp. kefirgranum subsp. nov. and emended 4165 description of L. kefiranofaciens Fujisawa et al. 1988. Int J Syst Evol Microbiol 54:551–6 4166 101. Takizawa S, Kojima S, Tamura S, Fujinaga S, Benno Y, Nakase T (1994) Lactobacillus kefirgranum 4167 sp. nov. and Lactobacillus parakefir sp. nov., two new species from kefir grains. Int J Syst 4168 Bacteriol 44:435–439 4169 102. Mukai T, Arihara K, Ikeda A, Nomura K, Suzuki F, Ohori H (2003) Lactobacillus kitasatonis sp. 4170 nov., from chicken intestine. Int J Syst Evol Microbiol 53:2055–9 4171 103. Rocha J, Botelho J, Ksiezarek M, et al (2020) Lactobacillus mulieris sp. nov., a new species of 4172 Lactobacillus delbrueckii group. Int J Syst Evol Microbiol in press 4173 104. Wang C, Huang Y, Li L, Guo J, Wu Z, Deng Y, Dai L, Ma S (2018) Lactobacillus panisapium sp. 4174 nov., from honeybee Apis cerana bee bread. Int J Syst Evol Microbiol 68:703–708 4175 105. Tanizawa Y, Tada I, Kobayashi H, et al (2018) Lactobacillus paragasseri sp. nov., a sister taxon 4176 of Lactobacillus gasseri, based on whole‐genome sequence analyses. Int J Syst Evol Microbiol 4177 68:3512–3517 4178 106. Kim J‐S, Choe H, Kim KM, Lee Y‐R, Rhee M‐S, Park D‐S (2018) Lactobacillus porci sp. nov., 4179 isolated from small intestine of a swine. Int J Syst Evol Microbiol 68:3118–3124 4180 107. Lawson PA, Wacher C, Hansson I, Falsen E, Collins MD (2001) Lactobacillus psittaci sp. nov., 4181 isolated from a hyacinth macaw (Anodorhynchus hyacinthinus). Int J Syst Evol Microbiol 4182 51:967–970 4183 108. Killer J, Havlik J, Vlkova E, Rada V, Pechar R, Benada O, Kope ny J, Kofro ova O, Sechovcova H 4184 (2014) Lactobacillus rodentium sp. nov., from the digestive tract of wild rodents. Int J Syst Evol 4185 Microbiol 64:1526–1533 4186 109. Wang L‐T, Kuo H‐P, Wu Y‐C, Tai C‐J, Lee F‐L (2009) Lactobacillus taiwanensis sp. nov., isolated 4187 from silage. Int J Syst Evol Microbiol 59:2064–2068 4188 110. Meng J, Jin D, Yang J, Lai X‐H, Pu J, Zhu W, Huang Y, Liang H, Lu S (2020) Lactobacillus 4189 xujianguonis sp. nov., isolated from faeces of Marmota himalayana. Int J Syst Evol Microbiol 4190 70:11–15 4191 111. Nakamura LK, Crowell CD (1979) Lactobacillus amylophilus, a new starch‐hydrolyzing species 4192 from swine waste‐corn fermentation. Dev Ind Microbiol 20:531–540 4193 112. Naser SM, Vancanneyt M, Snauwaert C, Vrancken G, Hoste B, De Vuyst L, Swings J (2006) 4194 Reclassification of Lactobacillus amylophilus LMG 11400 and NRRL B‐4435 as Lactobacillus 4195 amylotrophicus sp. nov. Int J Syst Evol Microbiol 56:2523–2527 4196 113. Killer J, Votavova A, Valterova I, Vlkova E, Rada V, Hroncova Z (2014) Lactobacillus bombi sp. 4197 nov., from the digestive tract of laboratory‐reared bumblebee queens (Bombus terrestris). Int 4198 J Syst Evol Microbiol 64:2611–2617 4199 114. Gänzle MG, Zheng J (2019) Lifestyles of sourdough lactobacilli – do they matter for microbial 4200 ecology and bread quality? Int J Food Microbiol 302:15–23 4201 115. Reuter G (1983) Lactobacillus alimentarius sp. nov., nom rev. and Lactobacillus farciminis sp. 4202 nov., nom. rev. Syst Appl Microbiol 4:277–279 4203 116. Lemay M‐J, Choquette J, Delaquis PJ, Gariépy C, Rodrigue N, Saucier L (2002) Antimicrobial 4204 effect of natural preservatives in a cooked and acidified chicken meat model. Int J Food 4205 Microbiol 78:217–226

110

4206 117. Jung MY, Lee SH, Lee M, Song JH, Chang JY (2017) Lactobacillus allii sp. nov. isolated from 4207 scallion kimchi. Int J Syst Evol Microbiol 67:4936–4942 4208 118. Wei YX, Gu CT (2019) Lactobacillus yilanensis sp. nov., Lactobacillus bayanensis sp. nov., 4209 Lactobacillus keshanensis sp. nov., Lactobacillus kedongensis sp. nov., Lactobacillus 4210 baiquanensis sp. nov., Lactobacillus jidongensis sp. nov., Lactobacillus hulinensis sp. nov., 4211 Lactobacillus mishanensis sp. nov. and Lactobacillus zhongbaensis sp. nov., isolated from 4212 Chinese traditional pickle and yogurt. Int J Syst Evol Microbiol 69:3183–3195 4213 119. Yang S‐J, Kim B‐Y, Chun J (2017) Rejection of reclassification of Lactobacillus kimchii and 4214 Lactobacillus bobalius as later subjective synonyms of Lactobacillus paralimentarius using 4215 comparative genomics. Int J Syst Evol Microbiol 67:4515–4517 4216 120. Manes‐Lazaro R, Ferrer S, Rodas AM, Urdiain M, Pardo I (2008) Lactobacillus bobalius sp. nov., 4217 a lactic acid bacterium isolated from Spanish Bobal grape must. Int J Syst Evol Microbiol 4218 58:2699–2703 4219 121. Scheirlinck I, Van der Meulen R, Van Schoor A, Huys G, Vandamme P, De Vuyst L, Vancanneyt 4220 M (2007) Lactobacillus crustorum sp. nov., isolated from two traditional Belgian wheat 4221 sourdoughs. Int J Syst Evol Microbiol 57:1461–1467 4222 122. Qian B, Yin L, Yao X, Zhong Y, Gui J, Lu F, Zhang F, Zhang J (2018) Effects of fermentation on the 4223 hemolytic activity and degradation of Camellia oleifera saponins by Lactobacillus crustorum 4224 and Bacillus subtilis. FEMS Microbiol Lett 365:fny014 4225 123. Chang C ‐h., Chen Y ‐s., Lee T ‐t., Chang Y ‐c., Yu B (2015) Lactobacillus formosensis sp. nov., a 4226 lactic acid bacterium isolated from fermented soybean meal. Int J Syst Evol Microbiol 65:101– 4227 106 4228 124. Irisawa T, Tanaka N, Kitahara M, Sakamoto M, Ohkuma M, Okada S (2014) Lactobacillus 4229 furfuricola sp. nov., isolated from Nukadoko, rice bran paste for Japanese pickles. Int J Syst Evol 4230 Microbiol 64:2902–2906 4231 125. Du X, Cao K, Tan M, Pan Q (2019) Lactobacillus futsaii subsp. chongqingii subsp. nov., Isolated 4232 from a traditional Chinese pickle. Curr Microbiol 76:153–158 4233 126. Chao S‐H, Kudo Y, Tsai Y‐C, Watanabe K (2012) Lactobacillus futsaii sp. nov., isolated from fu‐ 4234 tsai and suan‐tsai, traditional Taiwanese fermented mustard products. Int J Syst Evol Microbiol 4235 62:489–494 4236 127. Ximenes JCM, Hissa DC, Ribeiro LH, Rocha MVP, Oliveira EG, Melo VMM (2019) Sustainable 4237 recovery of protein‐rich liquor from shrimp farming waste by lactic acid fermentation for 4238 application in tilapia feed. Brazilian J Microbiol 50:195–203 4239 128. Jung H‐M, Liu Q‐M, Kim J‐K, Lee S‐T, Kim S‐C, Im W‐T (2013) Lactobacillus ginsenosidimutans 4240 sp. nov., isolated from kimchi with the ability to transform ginsenosides. Antonie Van 4241 Leeuwenhoek 103:867–876 4242 129. Schuster JA, Klingl A, Vogel RF, Ehrmann MA (2019) Polyphasic characterization of two novel 4243 Lactobacillus spp. isolated from blown salami packages: Description of Lactobacillus 4244 halodurans sp. nov. and Lactobacillus salsicarnum sp. nov. Syst Appl Microbiol 42:126023 4245 130. Gu CT, Li CY, Yang LJ, Huo GC (2013) Lactobacillus heilongjiangensis sp. nov., isolated from 4246 Chinese pickle. Int J Syst Evol Microbiol 63:4094–4099 4247 131. Fu ML, Gu CT (2019) Lactobacillus huachuanensis sp. nov., isolated from Chinese traditional 4248 pickle. Int J Syst Evol Microbiol 69:2807–2814 4249 132. Kröckel L, Ehrmann MA, Radmann P, Lick S, Vogel RF, Bantleon A (2016) Lactobacillus insicii sp. 4250 nov., isolated from fermented raw meat. Int J Syst Evol Microbiol 66:236–242

111

4251 133. Kim J, Kim JY, Kim M‐S, Roh SW, Bae J‐W (2013) Lactobacillus kimchiensis sp. nov., isolated from 4252 a fermented food. Int J Syst Evol Microbiol 63:1355–1359 4253 134. Park CS, Kho YH, Kang KH, Yoon JH, Kang SS, Park YH, Mheen TI, Ahn JS, Lee HJ, Kim TK (2000) 4254 Lactobacillus kimchii sp. nov., a new species from kimchi. Int J Syst Evol Microbiol 50:1789– 4255 1795 4256 135. Zhao W, Gu CT (2019) Lactobacillus terrae is a later heterotypic synonym of Lactobacillus 4257 metriopterae. Int J Syst Evol Microbiol 69:1597–1600 4258 136. Chiba M, Itabashi T, Hirai K, Sakamoto M, Ohkuma M, Ishige T, Kawasaki S (2018) Lactobacillus 4259 metriopterae sp. nov., a novel lactic acid bacterium isolated from the gut of grasshopper 4260 Metrioptera engelhardti. Int J Syst Evol Microbiol 68:1484–1489 4261 137. Ehrmann MA, Müller MRA, Vogel RF (2003) Molecular analysis of sourdough reveals 4262 Lactobacillus mindensis sp. nov. Int J Syst Evol Microbiol 53:7–13 4263 138. Chen Y, Wang L, Liao Y, Lan Y, Chang C, Chang Y, Wu H, Lo H, Otoguro M, Yanagida F (2017) 4264 Lactobacillus musae sp. nov., a novel lactic acid bacterium isolated from banana fruits. Int J 4265 Syst Evol Microbiol 67:5144–5149 4266 139. Valcheva R, Ferchichi MF, Korakli M, Ivanova I, Gänzle MG, Vogel RF, Prévost H, Onno B, 4267 Dousset X (2006) Lactobacillus nantensis sp. nov., isolated from French wheat sourdough. Int J 4268 Syst Evol Microbiol 56:587–591 4269 140. Kashiwagi T, Suzuki T, Kamakura T (2009) Lactobacillus nodensis sp. nov., isolated from rice 4270 bran. Int J Syst Evol Microbiol 59:83–86 4271 141. O’Brien E, Mills S, Dobson A, et al (2017) Contribution of the novel sulfur‐producing adjunct 4272 Lactobacillus nodensis to flavor development in Gouda cheese. J Dairy Sci 100:4322–4334 4273 142. Heo J, Saitou S, Tamura T, Cho H, Kim J‐S, Joa J‐H, Kim J‐S, Kwon S‐W, Kim S‐J (2018) Lactobacilus 4274 nuruki sp. nov., isolated from Nuruk, a Korean fermentation starter. Int J Syst Evol Microbiol 4275 68:3273–3278 4276 143. Cai Y, Okada H, Mori H, Benno Y, Nakase T (1999) Lactobacillus paralimentarius sp. nov., 4277 isolated from sourdough. Int J Syst Bacteriol 49:1451–1455 4278 144. Lin S‐T, Wang L‐T, Wang H‐M, Tamura T, Mori K, Huang L, Watanabe K (2019) Lactobacillus 4279 suantsaicola sp. nov. and Lactobacillus suantsaiihabitans sp. nov., isolated from suan‐tsai, a 4280 traditional fermented mustard green product of Taiwan. Int J Syst Evol Microbiol doi: 4281 10.1099/ijsem.0.003522 4282 145. Chenoll E, Carmen Macián M, Aznar R (2006) Lactobacillus tucceti sp. nov., a new lactic acid 4283 bacterium isolated from sausage. Syst Appl Microbiol 29:389–395 4284 146. Krockel L, Schillinger U, Franz C, Bantleon A, Ludwig W (2003) Lactobacillus versmoldensis sp. 4285 nov., isolated from raw fermented sausage. Int J Syst Evol Microbiol 53:513–517 4286 147. Zhang Z, Hou Q, Wang Y, Li W, Zhao H, Sun Z, Guo Z (2019) Lactobacillus zhachilii sp. nov., a 4287 lactic acid bacterium isolated from Zha‐Chili. Int J Syst Evol Microbiol 69:2196–2201 4288 148. Tong H, Dong X (2005) Lactobacillus concavus sp. nov., isolated from the walls of a distilled 4289 spirit fermenting cellar in China. Int J Syst Evol Microbiol 55:2199–2202 4290 149. Haakensen M, Dobson CM, Hill JE, Ziola B (2009) Reclassification of Pediococcus dextrinicus 4291 (Coster and White 1964) Back 1978 (Approved Lists 1980) as Lactobacillus dextrinicus comb. 4292 nov., and emended description of the genus Lactobacillus. Int J Syst Evol Microbiol 59:615–621 4293 150. Endo A, Okada S (2007) Lactobacillus composti sp. nov., a lactic acid bacterium isolated from a 4294 compost of distilled shochu residue. Int J Syst Evol Microbiol 57:870–872

112

4295 151. Torres‐Maravilla E, Lenoir M, Mayorga‐Reyes L, Allain T, Sokol H, Langella P, Sánchez‐Pardo 4296 ME, Bermúdez‐Humarán LG (2016) Identification of novel anti‐inflammatory probiotic strains 4297 isolated from pulque. Appl Microbiol Biotechnol 100:385–396 4298 152. Back W, Bohak I, Ehrmann M, Ludwig W, Pot B, Kersters K, Schleifer KH (1999) Lactobacillus 4299 perolens sp. nov., a soft drink spoilage bacterium. Syst Appl Microbiol 22:354–359 4300 153. Miyamoto M, Seto Y, Hao DH, Teshima T, Sun YB, Kabuki T, Yao LB, Nakajima H (2005) 4301 Lactobacillus harbinensis sp. nov., consisted of strains isolated from traditional fermented 4302 vegetables “Suan cai” in Harbin, Northeastern China and Lactobacillus perolens DSM 12745. 4303 Syst Appl Microbiol 28:688–94 4304 154. Zou Y, Liu F, Fang C, Wan D, Yang R, Su Q, Yang R, Zhao J (2013) Lactobacillus shenzhenensis sp. 4305 nov., isolated from a fermented dairy beverage. Int J Syst Evol Microbiol 63:1817–1823 4306 155. Tidall B (2008) The type strain of Lactobacillus casei is ATCC 393, ATCC 334 cannot serve as the 4307 type because it represents a different taxon, the name Lactobacillus paracasei and its 4308 subspecies names are not rejected and the revival of the name “Lactobacillus zeae” 4309 contravenes Rules 51b (1) and (2) of the International Code of Nomenclature of Bacteria. 4310 Opinion 82. Int J Syst Evol Microbiol 58:1764–5 4311 156. Orla‐Jensen S (1916) Maelkeri‐Bakteriologi. 4312 157. Hansen P, Lessel E (1971) Lactobacillus casei (Orla‐Jensen) comb. nov. Int J Syst Bacteriol 4313 21:69–71 4314 158. Long GY, Gu CT (2019) Lactobacillus jixianensis sp. nov., Lactobacillus baoqingensis sp. nov., 4315 Lactobacillus jiayinensis sp. nov., Lactobacillus zhaoyuanensis sp. nov., Lactobacillus 4316 lindianensis sp. nov., Lactobacillus huananensis sp. nov., Lactobacillus tangyuanensis sp. nov., 4317 Lactobacillus fuyuanensis sp. nov., Lactobacillus tongjiangensis sp. nov., Lactobacillus fujinensis 4318 sp. nov. and Lactobacillus mulengensis sp. nov.,. Int J Syst Evol Microbiol 69:2340–2353 4319 159. Volokhov D V., Amselle M, Beck BJ, Popham DL, Whittaker P, Wang H, Kerrigan E, Chizhikov VE 4320 (2012) Lactobacillus brantae sp. nov., isolated from faeces of Canada geese (Branta 4321 canadensis). Int J Syst Evol Microbiol 62:2068–2076 4322 160. Oren A, Garrity GM (2015) Validation List No. 166. List of new names and new combinations 4323 previously effectively, but not validly, published. Int J Syst Evol Microbiol 65:3763–3767 4324 161. Tanasupawa S, Pakdeeto A, Thawai C, Yukphan P, Okada S (2007) Identification of lactic acid 4325 bacteria from fermented tea leaves (miang) in Thailand and proposals of Lactobacillus 4326 thailandensissp. nov., Lactobacillus camelliae sp. nov. and Pediococcus siamensis sp. nov. J Gen 4327 Appl Microbiol 53:7–15 4328 162. Huang C‐H, Liou J‐S, Lee A‐Y, Tseng M, Miyashita M, Huang L, Watanabe K (2018) Polyphasic 4329 characterization of a novel species in the Lactobacillus casei group from cow manure of Taiwan: 4330 Description of L. chiayiensis sp. nov. Syst Appl Microbiol 41:270–278 4331 163. Oren A, Garrity GM (2018) Validation List No. 184. List of new names and new combinations 4332 previously effectively, but not validly, published. Int J Syst Evol Microbiol 68:3379–3393 4333 164. Zhao W, Gu CT (2019) Lactobacillus hulanensis sp. nov., isolated from suancai, a traditional 4334 Chinese pickle. Int J Syst Evol Microbiol 69:2147–2152 4335 165. Morlon‐Guyot J, Guyot JP, Pot B, de Haut IJ, Raimbault M (2009) Lactobacillus manihotivorans 4336 sp. nov., a new starch‐hydrolysing lactic acid bacterium Isolated during cassava sour starch 4337 fermentation. Int J Syst Bacteriol 48:1101–1109 4338 166. Cai Y, Pang H, Kitahara M, Ohkuma M (2012) Lactobacillus nasuensis sp. nov., a lactic acid 4339 bacterium isolated from silage, and emended description of the genus Lactobacillus. Int J Syst

113

4340 Evol Microbiol 62:1140–1144 4341 167. Liu B, Dong X (2002) Lactobacillus pantheris sp. nov., isolated from faeces of a jaguar. Int J Syst 4342 Evol Microbiol 52:1745–1748 4343 168. Collins MD, Phillips BA, Zanoni P (1989) Deoxyribonucleic acid homology studies of 4344 Lactobacillus casei, Lactobacillus paracasei sp. nov., subsp. paracasei and subsp. tolerans, and 4345 Lactobacillus rhamnosus sp. nov., comb. nov. Int J Syst Bacteriol 39:105–108 4346 169. Dal Bello F, Hertel C (2006) Oral cavity as natural reservoir for intestinal lactobacilli. Syst Appl 4347 Microbiol 29:69–76 4348 170. Abo‐Elnaga I, Kandler O (1965) Zur Taxonomie der Gattung Lactobacillus Beijerinck. I. Das 4349 Subgenus Streptobacterium Orla‐Jensen. Zentralblatt fur Bakteriol Parasitenkd Infekt und Hyg 4350 2:1–36 4351 171. Lam Nguyen DT, Cnockaert M, Van Hoorde K, De Brandt E, Snauwaert I, Snauwaert C, De Vuyst 4352 L, Le BT, Vandamme P (2013) Lactobacillus porcinae sp. nov., isolated from traditional 4353 Vietnamese nem chua. Int J Syst Evol Microbiol 63:1754–1759 4354 172. Hansen P (1968) Type strains of Lactobacillus species. A report by the taxonomic subcommittee 4355 on lactobacilli and closely related organisms. 76 pp 4356 173. Oki K, Kudo Y, Watanabe K (2012) Lactobacillus saniviri sp. nov. and Lactobacillus senioris sp. 4357 nov., isolated from human faeces. Int J Syst Evol Microbiol 62:601–607 4358 174. Weiss N, Schillinger U, Laternser M, Kandler O (1981) Lactobacillus sharpeae sp. nov. and 4359 Lactobacillus agilis sp. nov., two new species of homofermentative, meso‐diaminopimelic acid‐ 4360 containing lactobacilli. Zentralbl Mikrobiol Parasitenkd Infekt Hyg Abt I Orig 1:242–253 4361 175. Weiss N, Schillinger U, Laternser M, Kandler O (1982) Validation List N∘ 8. Int J Syst Bacteriol 4362 32:266–268 4363 176. Gu CT, Li CY, Yang LJ, Huo GC (2013) Lactobacillus mudanjiangensis sp. nov., Lactobacillus 4364 songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., isolated from Chinese 4365 traditional pickle and sourdough. Int J Syst Evol Microbiol 63:4698–4706 4366 177. Leisner JJ, Vancanneyt M, Goris J, Christensen H, Rusul G (2000) Description of 4367 Paralactobacillus selangorensis gen. nov., sp. nov., a new lactic acid bacterium isolated from 4368 chili bo, a Malaysian food ingredient. Int J Syst Evol Microbiol 50:19–24 4369 178. Haakensen M, Pittet V, Ziola B (2011) Reclassification of Paralactobacillus selangorensis Leisner 4370 et al. 2000 as Lactobacillus selangorensis comb. nov. Int J Syst Evol Microbiol 61:2979–2983 4371 179. Shaw BG, Harding CD (1984) A numerical taxonomic study of lactic acid bacteria from vacuum‐ 4372 packed beef, pork, lamb and bacon. J Appl Bacteriol 56:25–40 4373 180. Klein G, Dicks LMT, Pack A, Hack B, Zimmermann K, Dellaglio F, Reuter G (1996) Emended 4374 descriptions of Lactobacillus sake (Katagiri, Kitahara, and Fukami) and Lactobacillus curvatus 4375 (Abo‐Elnaga and Kandler): Numerical classification revealed by protein figerprinting and 4376 identification based on biochemical patterns and DNA‐DNA hybridizations. Int J Syst Bacteriol 4377 46:367–376 4378 181. Chaillou S, Lucquin I, Najjari A, Zagorec M, Champomier‐Vergès M‐C (2013) Population genetics 4379 of Lactobacillus sakei reveals three lineages with distinct evolutionary histories. PLoS One 4380 8:e73253 4381 182. Koort J, Vandamme P, Schillinger U, Holzapfel W, Björkroth J (2004) Lactobacillus curvatus 4382 subsp. melibiosus is a later synonym of Lactobacillus sakei subsp. carnosus. Int J Syst Evol 4383 Microbiol 54:1621–6

114

4384 183. Torriani S, Van Reenen GA, Klein G, Reuter G, Dellaglio F, Dicks LM (1996) Lactobacillus curvatus 4385 subsp. curvatus subsp. nov. and Lactobacillus curvatus subsp. melibiosus subsp. nov. and 4386 Lactobacillus sake subsp. sake subsp. nov. and Lactobacillus sake subsp. carnosus subsp. nov., 4387 new subspecies of Lactobacillus curvatus Abo‐Elnaga and Kandler 1965 and Lactobacillus sake 4388 Katagiri, Kitahara, and Fukami 1934 (Klein et al. 1996, emended descriptions), respectively. Int 4389 J Syst Bacteriol 46:1158–1163 4390 184. Cousin FJ, Lynch SM, Harris HMB, McCann A, Lynch DB, Neville BA, Irisawa T, Okada S, Endo A, 4391 O’Toole PW (2015) Detection and genomic characterization of motility in Lactobacillus 4392 curvatus: Confirmation of motility in a species outside the Lactobacillus salivarius clade. Appl 4393 Environ Microbiol 81:1297–1308 4394 185. Troili‐Petersson G (1903) Studien über die Mikroorganismen des schwedischen Güterkäses. 4395 Zentralbl Bakteriol Parasitenkd Infekt Hyg II 11:120–143 4396 186. Terán LC, Coeuret G, Raya R, Zagorec M, Champomier‐Vergès MC, Chaillou S (2018) 4397 Phylogenomic analysis of Lactobacillus curvatus reveals two lineages distinguished by genes 4398 for fermenting plant‐derived carbohydrates. Genome Biol Evol 10:1516–1525 4399 187. Ogawa M, Kaneuchi C, Murakami M, Hayashidani H, Kato Y, Sakala RM (2002) Lactobacillus 4400 fuchuensis sp. nov., isolated from vacuum‐packaged refrigerated beef. Int J Syst Evol Microbiol 4401 52:1151–1154 4402 188. Beck R, Weiss N, Winter J (1988) Lactobacillus graminis sp. nov., a new species of facultatively 4403 heterofermentative lactobacilli surviving at low pH in grass silage. Syst Appl Microbiol 10:279– 4404 283 4405 189. Tohno M, Kitahara M, Irisawa T, Masuda T, Uegaki R, Ohkuma M, Tajima K (2013) Description 4406 of Lactobacillus iwatensis sp. nov., isolated from orchardgrass (Dactylis glomerata L.) silage, 4407 and Lactobacillus backii sp. nov. Int J Syst Evolyutionary Microbiol 63:3854–3860 4408 190. Yamada Y, Tahara Y (1984) Validation list No.14. J Gen Appl Microbiol 34:270 4409 191. Kandler O, Schillinger U, Weiss N (1983) Lactobacillus bifermentans sp. nov., nom. rev., an 4410 organism forming CO2 and H2 from lactic acid. Syst Appl Microbiol 4:408–412 4411 192. Chenoll E, Macián C, Aznar R (2006) Lactobacillus rennini sp. nov., isolated from rennin and 4412 associated with cheese spoilage. Int J Syst Evol Microbiol 56:449–452 4413 193. Kato Y, Sakala RM, Hayashidani H, Kiuchi A, Kaneuchi C, Ogawa M (2000) Lactobacillus algidus 4414 sp. nov., a psychrophilic lactic acid bacterium isolated from vacuum‐packaged refrigerated 4415 beef. Int J Syst Evol Microbiol 50:1143–1149 4416 194. Bechtner J, Wefers D, Schmid J, Vogel RF, Jakob F (2019) Identification and comparison of two 4417 closely related dextransucrases released by water kefir borne Lactobacillus hordei TMW 1.1822 4418 and Lactobacillus nagelii TMW 1.1827. Microbiology 165:956–966 4419 195. Carr JG, Davies PA (1970) Homofermentative lactobacilli of ciders including Lactobacillus mali 4420 nov. spec. J Appl Bacteriol 33:768–774 4421 196. Kaneuchi C, Seki M, Komagata K (1988) Taxonomic study of Lactobacillus mali Carr and Davis 4422 1970 and related strains: Validation of Lactobacillus mali Carr and Davis 1970 over Lactobacillus 4423 yamanashiensis Nonomura 1983. Int J Syst Bacteriol 38:269–272 4424 197. Mañes‐Laázaro R, Song J, Pardo I, Cho JC, Ferrer S (2009) Lactobacillus aquaticus sp. nov., 4425 isolated from a Korean freshwater pond. Int J Syst Evol Microbiol 59:2215–2218 4426 198. De Bruyne K, Camu N, De Vuyst L, Vandamme P (2009) Lactobacillus fabifermentans sp. nov. 4427 and Lactobacillus cacaonum sp. nov., isolated from Ghanaian cocoa fermentations. Int J Syst 4428 Evol Microbiol 59:7–12

115

4429 199. Chao SH, Tomii Y, Sasamoto M, Fujimoto J, Tsai YC, Watanabe K (2008) Lactobacillus capillatus 4430 sp. nov., a motile bacterium isolated from stinky tofu brine. Int J Syst Evol Microbiol 58:2555– 4431 2559 4432 200. Nielsen DS, Schillinger U, Franz CMAP, Bresciani J, Amoa‐Awua W, Holzapfel WH, Jakobsen M 4433 (2007) Lactobacillus ghanensis sp. nov., a motile lactic acid bacterium isolated from Ghanaian 4434 cocoa fermentations. Int J Syst Evol Microbiol 57:1468–1472 4435 201. Rouse S, Canchaya C, van Sinderen D (2008) Lactobacillus hordei sp. nov., a bacteriocinogenic 4436 strain isoloated from malted barley. Int J Syst Evol Microbiol 58:2013–2017 4437 202. Edwards CG, Collins MD, Lawson PA, Rodriguez A V (2000) Lactobacillus nagelii sp. nov., an 4438 organism isolated from a partially fermented wine. Int J Syst Evol Microbiol 50:699–702 4439 203. Manes‐Lazaro R, Ferrer S, Rossello‐Mora R, Pardo I (2009) Lactobacillus oeni sp. nov., from 4440 wine. Int J Syst Evol Microbiol 59:2010–2014 4441 204. Endo A, Okada S (2005) Lactobacillus satsumensis sp. nov., isolated from mashes of shochu, a 4442 traditional Japanese distilled spirit made from fermented rice and other starchy materials. Int 4443 J Syst Evol Microbiol 55:83–85 4444 205. Puertas AI, Arahal DR, Ibarburu I, Elizaquível P, Aznar R, Teresa DueñAs M (2014) Lactobacillus 4445 sicerae sp. nov., a lactic acid bacterium isolated from Spanish natural cider. Int J Syst Evol 4446 Microbiol 64:2949–2955 4447 206. Irisawa T, Okada S (2009) Lactobacillus sucicola sp. nov., a motile lactic acid bacterium isolated 4448 from oak tree (Quercus sp.) sap. Int J Syst Evol Microbiol 59:2662–2665 4449 207. Mañes‐Lázaro R, Ferrer S, Rosselló‐Mora R, Pardo I (2008) Lactobacillus uvarum sp. nov. – A 4450 new lactic acid bacterium isolated from Spanish Bobal grape must. Syst Appl Microbiol 31:425– 4451 433 4452 208. Rodas AM, Chenoll E, Macián MC, Ferrer S, Pardo I, Aznar R (2006) Lactobacillus vini sp. nov., a 4453 wine lactic acid bacterium homofermentative for pentoses. Int J Syst Evol Microbiol 56:513– 4454 517 4455 209. Kandler O (1983) Carbohydrate metabolism in lactic acid bacteria. Antonie Van Leeuwenhoek 4456 49:209–224 4457 210. Kakimoto S, Okazaki K, Sakane T, Imai K, Sumino Y, Akiyama S, Nakao Y (1989) Isolation and 4458 taxonomie characterization of acid urease‐producing bacteria. Agric Biol Chem 53:1111–1117 4459 211. Krumbeck JA, Marsteller NL, Frese SA, Peterson DA, Ramer‐Tait AE, Hutkins RW, Walter J (2016) 4460 Characterization of the ecological role of genes mediating acid resistance in Lactobacillus 4461 reuteri during colonization of the gastrointestinal tract. Environ Microbiol 18:2172–2184 4462 212. Li Y, Raftis E, Canchaya C, Fitzgerald GF, Sinderen D van, O’Toole PW, Van Sinderen D, O’Toole 4463 PW (2006) Polyphasic analysis indicates that Lactobacillus salivarius subsp. salivarius and 4464 Lactobacillus salivarius subsp. salicinius do not merit separate subspecies status. Int J Syst Evol 4465 Microbiol 56:2397–2403 4466 213. Raftis EJ, Salvetti E, Torriani S, Felis GE, O’Toole PW (2011) Genomic diversity of Lactobacillus 4467 salivarius. Appl Environ Microbiol 77:954–965 4468 214. Naser SM, Vancanneyt M, Hoste B, Snauwaert C, Swings J (2006) Lactobacillus cypricasei 4469 Lawson et al. 2001 is a later heterotypic synonym of Lactobacillus acidipiscis Tanasupawat et 4470 al. 2000. Int J Syst Evol Microbiol 56:1681–1683 4471 215. Tanasupawat S, Shida O, Okada S, Komagata K (2000) Lactobacillus acidipiscis sp. nov. and 4472 sp. nov., isolated from fermented fish in Thailand. Int J Syst Evol

116

4473 Microbiol 50:1479–1485 4474 216. Dent V, Williams R (1982) Lactobacillus animalis sp. nov., a new species of Lactobacillus from 4475 the alimentary canal of animals. Zentralbl Bakteriol Parasitenkd Infekt Hyg I Abt Orig C 3:377– 4476 386 4477 217. Osawa R, Fujisawa T, Pukall R (2006) Lactobacillus apodemi sp. nov., a tannase‐producing 4478 species isolated from wild mouse faeces. Int J Syst Evol Microbiol 56:1693–1696 4479 218. Vela AI, Fernandez A, Espinosa de los Monteros A, Goyache J, Herraez P, Tames B, Cruz F, 4480 Domínguez L, Fernández‐Garayzábal JF (2008) Lactobacillus ceti sp. nov., isolated from beaked 4481 whales (Ziphius cavirostris). Int J Syst Evol Microbiol 58:891–894 4482 219. Morotomi M, Yuki N, Kado Y, Kushiro A, Shimazaki T, Watanabe K, Yuyama T (2002) 4483 Lactobacillus equi sp. nov., a predominant intestinal Lactobacillus species of the horse isolated 4484 from faeces of healthy horses. Int J Syst Evol Microbiol 52:211–214 4485 220. Endo A, Irisawa T, Futagawa‐Endo Y, Salminen S, Ohkuma M, Dicks L (2013) Lactobacillus faecis 4486 sp.nov., isolated from animal faeces. Int J Syst Evol Microbiol 63:4502–4507 4487 221. Morita H, Shiratori C, Murakami M, et al (2007) Lactobacillus hayakitensis sp. nov., isolated 4488 from intestines of healthy thoroughbreds. Int J Syst Evol Microbiol 57:2836–2839 4489 222. Hemme D, Raibaud P, Ducluzeau R, Galpin J, Sicard P, van Heijenoort J (1980) Lactobacillus 4490 murinus n. sp., une nouvelle espèce de la flore dominante autochtone du tube digestif du rat 4491 et de la souris. Ann Microbiol 131A:297–308 4492 223. Chen YS, Miyashita M, Suzuki KI, Sato H, Hsu JS, Yanagida F (2010) Lactobacillus pobuzihii sp. 4493 nov., isolated from pobuzihi (fermented cummingcordia). Int J Syst Evol Microbiol 60:1914– 4494 1917 4495 224. Sharpe ME, Latham MJ, Garvie EI, Zirngibl J, Kandler O (1973) Two new species of Lactobacillus 4496 isolated from the bovine rumen, Lactobacillus ruminis sp.nov. and Lactobacillus vitulinus 4497 sp.nov. J Gen Microbiol 77:37–49 4498 225. O’ Donnell MM, Harris HMB, Lynch DB, Ross RP, O’Toole PW (2015) Lactobacillus ruminis 4499 strains cluster according to their mammalian gut source. BMC Microbiol 15:80 4500 226. Pedersen C, Roos S (2004) Lactobacillus saerimneri sp. nov., isolated from pig faeces. Int J Syst 4501 Evol Microbiol 54:1365–1368 4502 227. Tanizawa Y, Sakamoto M, Nakamura Y, Ohkuma M, Kojima Y, Kobayashi H, Tohno M (2019) 4503 Lactobacillus salitolerans sp. nov., a novel lactic acid bacterium isolated from spent mushroom 4504 substrates. Int J Syst Evol Microbiol 69:964–969 4505 228. Torriani S, Felis GE, Dellaglio F (2001) Differentiation of Lactobacillus plantarum, L. pentosus, 4506 and L. paraplantarum by recA gene sequence analysis and multiplex PCR assay with recA gene‐ 4507 derived primers. Appl Environ Microbiol 67:3450–3454 4508 229. Bringel F, Castioni A, Olukoya DK, Felis GE, Torriani S, Dellaglio F (2005) Lactobacillus plantarum 4509 subsp. argentoratensis subsp. nov., isolated from vegetable matrices. Int J Syst Evol Microbiol 4510 55:1629–1634 4511 230. Martino ME, Bayjanov JR, Caffrey BE, Wels M, Joncour P, Hughes S, Gillet B, Kleerebezem M, 4512 van Hijum SAFTFT, Leulier F (2016) Nomadic lifestyle of Lactobacillus plantarum revealed by 4513 comparative genomics of 54 strains isolated from different habitats. Environ Microbiol 4514 18:4974–4989 4515 231. Bergey DH, Harrison F, Breed R, Hammer F (1923) Bergey’s manual of determinative 4516 bacteriology, 1st ed. The Williams & Wilkins Co., Baltimore, pre

117

4517 232. Storelli G, Strigini M, Grenier T, Bozonnet L, Schwarzer M, Daniel C, Matos R, Leulier F (2018) 4518 Drosophila perpetuates nutritional mutualism by promoting the fitness of its intestinal 4519 symbiont Lactobacillus plantarum. Cell Metab 27:362‐377.e8 4520 233. Liu DD, Gu CT (2019) Lactobacillus pingfangensis sp. nov., Lactobacillus daoliensis sp. nov., 4521 Lactobacillus nangangensis sp. nov., Lactobacillus daowaiensis sp. nov., Lactobacillus 4522 dongliensis sp. nov., Lactobacillus songbeiensis sp. nov. and Lactobacillus kaifaensis sp. nov., 4523 isolated from traditional Chinese pickle. Int J Syst Evol Microbiol 69:3251–3261 4524 234. Mao Y, Chen M, Horvath P (2015) Lactobacillus herbarum sp. nov., a species related to 4525 Lactobacillus plantarum. Int J Syst Evol Microbiol 65:4682–4688 4526 235. Miyashita M, Yukphan P, Chaipitakchonlatarn W, et al (2015) Lactobacillus plajomi sp. nov. and 4527 Lactobacillus modestisalitolerans sp. nov., isolated from traditional fermented foods. Int J Syst 4528 Evol Microbiol 65:2485–2490 4529 236. Wuyts S, Van Beeck W, Oerlemans EFM, Wittouck S, Claes IJJ, De Boeck I, Weckx S, Lievens B, 4530 De Vuyst L, Lebeer S (2018) Carrot juice fermentations as man‐made microbial ecosystems 4531 dominated by lactic acid bacteria. Appl Environ Microbiol 84:00134–18 4532 237. Curk M‐C, Hubert J, Bringel F (1996) Lactobacillus paraplantarum sp.nov., a new species related 4533 to Lactobacillus plantarum. Int J Syst Bacteriol 46:595–598 4534 238. Zanoni P, Farrow JAE, Phillips BA, Collins MD (1987) Lactobacillus pentosus (Fred, Peterson, and 4535 Anderson) sp. nov., nom. rev. Int J Syst Bacteriol 37:339–341 4536 239. Gu CT, Wang F, Li CY, Liu F, Huo GC (2012) Lactobacillus xiangfangensis sp. nov., isolated from 4537 Chinese pickle. Int J Syst Evol Microbiol 62:860–863 4538 240. Ripari V, Bai Y, Gänzle MG (2019) Metabolism of phenolic acids in whole wheat and rye malt 4539 sourdoughs. Food Microbiol 77:43–51 4540 241. Gaur G, Oh J‐H, Filannino P, Gobbetti M, van Pijkeren J‐P, Gänzle MG (2020) Genetic 4541 determinants of hydroxycinnamic acid metabolism in heterofermentative lactobacilli. Appl 4542 Environ Microbiol 86:e02461‐19 4543 242. Corsetti A, Settanni L, van Sinderen D, Felis GE, Dellaglio F, Gobbetti M (2005) Lactobacillus 4544 rossii sp. nov., isolated from wheat sourdough. Int J Syst Evol Microbiol 55:35–40 4545 243. Filannino P, Cavoski I, Thlien N, Vincentini O, De Angelis M, Silano M, Gobbetti M, Di Cagno R 4546 (2016) Lactic acid fermentation of cactus cladodes (Opuntia ficus‐indica L.) generates flavonoid 4547 derivatives with and anti‐Inflammatory properties. PLoS One 11:e0152575 4548 244. Asakawa Y, Takesue N, Asano S, Shimotsu S, Iijima K, Suzuki K, Motoyama Y, Aizawa M (2017) 4549 Lactobacillus curtus sp. nov., isolated from beer in Finland. Int J Syst Evol Microbiol 67:3899– 4550 3906 4551 245. Aslam Z, Im W‐T, Ten LN, Lee M, Kim K‐H, Lee S‐T (2006) Lactobacillus siliginis sp. nov., isolated 4552 from wheat sourdough in South Korea. Int J Syst Evol Microbiol 56:2209–2213 4553 246. Dellaglio F, Vancanneyt M, Endo A, Vandamme P, Felis GE, Castioni A, Fujimoto J, Watanabe K, 4554 Okada S (2006) Lactobacillus durianis Leisner et al. 2002 is a later heterotypic synonym of 4555 Lactobacillus vaccinostercus Kozaki and Okada 1983. Int J Syst Evol Microbiol 56:1721–1724 4556 247. Okada S, Suzuki Y, Kozaki M (1979) A new heterofermentative Lactobacillus species withmeso‐ 4557 diaminopimelic acid in peptidoglycan, Lactobacillus vaccinostercus Kozaki and Okada sp. no. J 4558 Gen Appl Microbiol 25:215–221 4559 248. Tohno M, Kitahara M, Uegaki R, Irisawa T, Ohkuma M, Tajima K (2013) Lactobacillus 4560 hokkaidonensis sp. nov., isolated from subarctic timothy grass (Phleum pratense L.) silage. Int

118

4561 J Syst Evol Microbiol 63:2526–2531 4562 249. Koort J, Murros A, Coenye T, Eerola S, Vandamme P, Sukura A, Björkroth J (2005) Lactobacillus 4563 oligofermentans sp. nov., associated with spoilage of modified‐atmosphere‐packaged poultry 4564 products. Appl Environ Microbiol 71:4400–6 4565 250. Kleynmans U, Heinzl H, Hammes WP (1989) Lactobacillus suebicus sp. nov., an obligately 4566 heterofermentative Lactobacillus species isolated from fruit mashes. Syst Appl Microbiol 4567 11:267–271 4568 251. Oberg TS, Oberg CJ, Culumber MD, Ortakci F, Broadbent JR, McMahon DJ (2016) Lactobacillus 4569 wasatchensis sp. nov., a non‐starter lactic acid bacteria isolated from aged Cheddar cheese. Int 4570 J Syst Evol Microbiol 66:158–164 4571 252. Teixeira JS, Seeras A, Sanchez‐Maldonado AF, Zhang C, Su MSW, Gänzle MG (2014) Glutamine, 4572 glutamate, and arginine‐based acid resistance in Lactobacillus reuteri. Food Microbiol 42:172– 4573 180 4574 253. Tieking M, Kaditzky S, Valcheva R, Korakli M, Vogel RF, Gänzle MG (2005) Extracellular 4575 and oligosaccharides from intestinal lactobacilli. J Appl Microbiol 4576 99:692–702 4577 254. Dellaglio F, Torriani S, Felis GE (2004) Reclassification of Lactobacillus cellobiosus Rogosa et al. 4578 1953 as a later synonym of Lactobacillus fermentum Beijerinck 1901. Int J Syst Evol Microbiol 4579 54:809–812 4580 255. Beijerinck M. (1901) Anhäufungsversuche mit Ureumbakterien. Ureumspaltung durch Urease 4581 und durch Katabolismus. Zentralbl Bakteriol Parasitenkd Infekt Hyg II Abt 7:33–61 4582 256. Kim H‐J, Eom S‐J, Park S‐J, Cha C‐J, Kim G‐B (2011) Lactobacillus alvi sp. nov., isolated from the 4583 intestinal tract of chicken. FEMS Microbiol Lett 323:83–7 4584 257. Killer J, Pechar R, Švec P, Salmonová H, Švejstil R, Geigerová M, Rada V, Vlková E, Mekadim C 4585 (2017) Lactobacillus caviae sp. nov., an obligately heterofermentative bacterium isolated from 4586 the oral cavity of a Guinea pig (Cavia aperea f. porcellus). Int J Syst Evol Microbiol 67:2903– 4587 2909 4588 258. Nikolaitchouk N, Wacher C, Falsen E, Andersch B, Collins MD, Lawson PA (2001) Lactobacillus 4589 coleohominis sp. nov., isolated from human sources. Int J Syst Evol Microbiol 51:2081–2085 4590 259. Endo A, Roos S, Satoh E, Morita H, Okada S (2008) Lactobacillus equigenerosi sp. nov., a coccoid 4591 species isolated from faeces of thoroughbred racehorses. Int J Syst Evol Microbiol 58:914–918 4592 260. Müller MRA, Ehrmann MA, Vogel RF (2000) Lactobacillus frumenti sp. nov., a new lactic acid 4593 bacterium isolated from rye‐bran fermentations with a long fermentation period. Int J Syst Evol 4594 Microbiol 50:2127–2133 4595 261. Tsuchida S, Kitahara M, Nguema PPM, Norimitsu S, Fujita S, Yamagiwa J, Ngomanda A, Ohkuma 4596 M, Ushida K (2014) Lactobacillus gorillae sp. nov., isolated from the faeces of captive and wild 4597 western lowland gorillas (Gorilla gorilla gorilla). Int J Syst Evol Microbiol 64:4001–4006 4598 262. Felis GE, Vancanneyt M, Snauwaert C, Swings J, Torriani S, Castioni A, Dellaglio F (2006) 4599 Reclassification of Lactobacillus thermotolerans Niamsup et al. 2003 as a later synonym of 4600 Lactobacillus ingluviei Baele et al. 2003. Int J Syst Evol Microbiol 56:793–795 4601 263. Baele M, Vancanneyt M, Devriese LA, Lefebvre K, Swings J, Haesebrouck F (2003) Lactobacillus 4602 ingluviei sp. nov., isolated from the intestinal tract of pigeons. Int J Syst Evol Microbiol 53:133– 4603 136 4604 264. Roos S, Karner F, Axelsson L, Jonsson H (2000) Lactobacillus mucosae sp. nov., a new species

119

4605 with in vitro mucus‐ binding activity isolated from pig intestine. Int J Syst Evol Microbiol 4606 50:251–258 4607 265. Farrow JAE, Collins MD (1988) Notes: Lactobacillus oris sp. nov. from the human oral cavity. Int 4608 J Syst Bacteriol 38:116–118 4609 266. Wiese BG, Stohmar W, Rainey FA, Diekmann H (2009) Lactobacillus panis sp. nov., from 4610 sourdough with a long fermentation period. Int J Syst Bacteriol 46:449–453 4611 267. Vogel RF, Böcker G, Stolz P, Ehrmann M, Fanta D, Ludwig W, Pot B, Kersters K, Schleifer KH, 4612 Hammes WP (2009) Identification of lactobacilli from sourdough and description of 4613 Lactobacillus pontis sp. nov. Int J Syst Bacteriol 44:223–229 4614 268. Kandler O, Stetter K‐O, Köhl R (1980) Lactobacillus reuteri sp. nov., a new species of 4615 heterofermentative lactobacilli. Zentralbl Bakteriol Hyg Abt IOrig C 1:264–269 4616 269. Duar RM, Frese SA, Lin XB, et al (2017) Experimental evaluation of host adaptation of 4617 Lactobacillus reuteri to different vertebrate species. Appl Environ Microbiol 83:e00132‐17 4618 270. Frese SA, Benson AK, Tannock GW, et al (2011) The evolution of host specialization in the 4619 vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet 7:e1001314 4620 271. Frese S, MacKenzie D, Peterson D, et al (2013) Molecular characterization of host‐specific 4621 biofilm formation in a vertebrate gut symbiont. PLoS Genet 9:e1004057 4622 272. Lin XB, Lohans CT, Duar R, Zheng J, Vederas JC, Walter J, Gänzle M (2015) Genetic determinants 4623 of reutericyclin biosynthesis in Lactobacillus reuteri. Appl Environ Microbiol 81:2032–41 4624 273. Zheng J, Zhao X, Lin XB, Gänzle M (2016) Comparative genomics Lactobacillus reuteri from 4625 sourdough reveals adaptation of an intestinal symbiont to food fermentations. Sci Rep 5:18234 4626 274. Ehrmann MA, Brandt M, Stolz P, Vogel RF, Korakli M (2007) Lactobacillus secaliphilus sp. nov., 4627 isolated from type II sourdough fermentation. Int J Syst Evol Microbiol 57:745–750 4628 275. Enbley TM, Faquir N, Bossart W, Collins MD (1989) Lactobacillus vaginalis sp. nov. from the 4629 human vagina. Int J Syst Bacteriol 39:368–370 4630 276. Afouda P, Fournier PE, Raoult D, Merhej V (2017) ‘Lactobacillus timonensis’ sp. nov., a new 4631 bacterial species isolated from the human gut. New Microbes New Infect 19:121–122 4632 277. Russell C, Walker TK (1953) Lactobacillus malefermentans n.sp., isolated from beer. J Gen 4633 Microbiol 8:160–162 4634 278. Farrow JAE, Phillips BA, Collins MD (1988) Nucleic acid studies on some heterofermentative 4635 lactobacilli: Description of Lactobacillus malefermentans sp.nov. and Lactobacillus 4636 parabuchneri sp.nov. FEMS Microbiol Lett 55:163–168 4637 279. Carr JG, Davies PA (1972) The ecology and classification of strains of Lactobacillus collinoides 4638 nov. spec.: a bacterium commonly found in fermenting apple juice. J Appl Bacteriol 35:463– 4639 471 4640 280. Liang Z‐Q, Srinivasan S, Kim Y‐J, Kim H‐B, Wang H‐T, Yang D‐C (2011) Lactobacillus kimchicus 4641 sp. nov., a ‐glucosidase‐producing bacterium isolated from kimchi. Int J Syst Evol Microbiol 4642 61:894–897 4643 281. Tohno M, Kitahara M, Irisawa T, Ohmori H, Masuda T, Ohkum M, Tajima K (2015) Lactobacillus 4644 mixtipabuli sp. nov. isolated from total mixed ration silage. Int J Syst Evol Microbiol 65:1981– 4645 1985 4646 282. Chao S‐H, Sasamoto M, Kudo Y, Fujimoto J, Tsai Y‐C, Watanabe K (2010) Lactobacillus 4647 odoratitofui sp. nov., isolated from stinky tofu brine. Int J Syst Evol Microbiol 60:2903–2907

120

4648 283. Tohno M, Kitahara M, Irisawa T, Inoue H, Uegaki R, Ohkuma M, Tajima K (2013) Lactobacillus 4649 oryzae sp. nov., isolated from fermented rice grain (Oryza sativa L. subsp. japonica). Int J Syst 4650 Evol Microbiol 63:2957–2962 4651 284. Ehrmann MA, Vogel RF (2005) Taxonomic note “Lactobacillus pastorianus” (Van Laer, 1892) a 4652 former synonym for Lactobacillus paracollinoides. Syst Appl Microbiol 28:54–56 4653 285. Suzuki K, Funahashi W, Koyanagi M, Yamashita H (2004) Lactobacillus paracollinoides sp. nov., 4654 isolated from brewery environments. Int J Syst Evol Microbiol 54:115–117 4655 286. Tohno M, Tanizawa Y, Irisawa T, Masuda T, Sakamoto M, Arita M, Ohkuma M, Kobayashi H 4656 (2017) Lactobacillus silagincola sp. nov. and Lactobacillus pentosiphilus sp. nov., isolated from 4657 silage. Int J Syst Evol Microbiol 67:3639–3644 4658 287. Tohno M, Kitahara M, Irisawa T, Masuda T, Uegaki R, Ohkuma M, Tajima K (2013) Lactobacillus 4659 silagei sp. nov., isolated from orchardgrass silage. Int J Syst Evol Microbiol 63:4613–4618 4660 288. Kitahara M, Sakamoto M, Benno Y (2010) Lactobacillus similis sp. nov., isolated from fermented 4661 cane molasses. Int J Syst Evol Microbiol 60:187–190 4662 289. Bergey DH, Breed RS, Hammer BW, Huntoon FM, Murray EGD, Harrison FC (1934) Bergey’s 4663 Manual of Determinative Bacteriology, 4th ed. The Williams & Wilkins Co., Baltimore 4664 290. Fraunhofer ME, Geißler AJ, Behr J, Vogel RF (2019) Comparative genomics of Lactobacillus 4665 brevis reveals a significant plasmidome overlap of brewery and insect isolates. Curr Microbiol 4666 76:37–47 4667 291. Vancanneyt M, Neysens P, Wachter M De, et al (2005) Lactobacillus acidifarinae sp. nov. and 4668 Lactobacillus zymae sp. nov., from wheat sourdoughs. Int J Syst Evol Microbiol 55:615–620 4669 292. Guu J‐R, Wang L‐T, Hamada M, Wang C, Lin R‐W, Huang L, Watanabe K (2018) Lactobacillus 4670 bambusae sp. nov., isolated from traditional fermented ma bamboo shoots in Taiwan. Int J Syst 4671 Evol Microbiol 68:2424–2430 4672 293. Koob J, Jacob F, Wenning M, Hutzler M (2017) Lactobacillus cerevisiae sp. nov., isolated from a 4673 spoiled brewery sample. Int J Syst Evol Microbiol 67:3452‐3457. 4674 294. Valcheva R, Korakli M, Onno B, Prévost H, Ivanova I, Ehrmann MA, Dousset X, Gänzle MG, Vogel 4675 RF (2005) Lactobacillus hammesii sp. nov., isolated from French sourdough. Int J Syst Evol 4676 Microbiol 55:763–767 4677 295. Black BA, Zannini E, Curtis JM, Gänzle MG (2013) Antifungal hydroxy fatty acids produced 4678 during sourdough fermentation: Microbial and enzymatic pathways, and antifungal activity in 4679 bread. Appl Environ Microbiol 79:1866–1873 4680 296. Bui TPN, Kim Y‐J, In J‐G, Yang D‐C (2011) Lactobacillus koreensis; sp. nov., isolated from the 4681 traditional Korean food kimchi. Int J Syst Evol Microbiol 61:772–776 4682 297. Scheirlinck I, Van der Meulen R, Van Schoor A, Cleenwerck I, Huys G, Vandamme P, De Vuyst L, 4683 Vancanneyt M (2007) Lactobacillus namurensis sp. nov., isolated from a traditional Belgian 4684 sourdough. Int J Syst Evol Microbiol 57:223–227 4685 298. Vancanneyt M, Naser SM, Engelbeen K, De Wachter M, Van der Meulen R, Cleenwerck I, Hoste 4686 B, Vuyst L De, Swings J (2006) Reclassification of Lactobacillus brevis strains LMG 11494 and 4687 LMG 11984 as Lactobacillus parabrevis sp. nov. Int J Syst Evol Microbiol 56:1553–1557 4688 299. Ehrmann MA, Preissler P, Danne M, Vogel RF (2010) Lactobacillus paucivorans sp. nov., isolated 4689 from a brewery environment. Int J Syst Evol Microbiol 60:2353–2357 4690 300. Hiraga K, Ueno Y, Sukontasing S, Tanasupawat S, Oda K (2008) Lactobacillus senmaizukei sp. 4691 nov., isolated from Japanese pickle. Int J Syst Evol Microbiol 58:1625–1629

121

4692 301. Meroth CB, Hammes WP, Hertel C (2004) Characterisation of the microbiota of rice sourdoughs 4693 and description of Lactobacillus spicheri sp. nov. Syst Appl Microbiol 27:151–159 4694 302. Liou J‐S, Huang C‐H, Wang C‐L, Lee A‐Y, Mori K, Tamura T, Watanabe M, Blom J, Huang L, 4695 Watanabe K (2019) Lactobacillus suantsaii sp. nov., isolated from suan‐tsai, a traditional 4696 Taiwanese fermented mustard green. Int J Syst Evol Microbiol 69:1484–1489 4697 303. Yi EJ, Yang JE, Lee JM, Park YJ, Park SY, Shin HS, Kook MC, Yi TH (2013) Lactobacillus yonginensis 4698 sp. nov., a lactic acid bacterium with ginsenoside converting activity isolated from Kimchi. Int J 4699 Syst Evol Microbiol 63:3274–3279 4700 304. Charlton DB, Nelson ME, Werkman CH (1934) Physiology of Lactobacillus fructivorans sp. nov. 4701 isolated from spoiled salad dressing. Iowa State J Sci 9:1–11 4702 305. Weiss N, Schillinger U, Kandler O (1984) Lactobacillus trichodes , and Lactobacillus 4703 heterohiochii, Subjective Synonyms of Lactobacillus fructivorans. Syst Appl Microbiol 4:507– 4704 511 4705 306. Zhao W, Gu CT (2019) Lactobacillus homohiochii is a later heterotypic synonym of Lactobacillus 4706 fructivorans. Int J Syst Evol Microbiol 69:17201–17234 4707 307. Kitahara K, Kaneko T, Goto O (1957) Taxonomic studies on the hiochi‐bacteria, specific 4708 saprophytes of sake. II. Identification and classification of hiochi‐bacteria. J Gen Appl Microbiol 4709 3:111–120 4710 308. Suzuki K, Asano S, Ijima K, Kitamoto K (2008) Sake and beer spoilage lactic acid bacteria – a 4711 review. J Inst Brew 114:209–223 4712 309. Wong CNA, Ng P, Douglas AE (2011) Low‐diversity bacterial community in the gut of the fruitfly 4713 Drosophila melanogaster. Environ Microbiol 13:1889–1900 4714 310. Endo A, Futagawa‐Endo Y, Sakamoto M, Kitahara M, Dicks LMT (2010) Lactobacillus florum sp. 4715 nov., a fructophilic species isolated from flowers. Int J Syst Evol Microbiol 60:2478–2482 4716 311. Techo S, Miyashita M, Shibata C, Tanaka N, Wisetkhan P, Visessanguan W, Tanasupawat S 4717 (2016) Lactobacillus ixorae sp. nov., isolated from a flower (West‐Indian Jasmine). Int J Syst 4718 Evol Microbiol 66:5500–5505 4719 312. Back W, Bohak I, Ehrmann M, Ludwig W, Schleifer KH (1996) Revival of the species Lactobacillus 4720 lindneri and the design of a species specific oligonucleotide probe. Syst Appl Microbiol 19:322– 4721 325 4722 313. Kline L, Sugihara TF (1971) Isolation and characterization of undescribed bacterial species 4723 responsible for the souring activity. Appl Microbiol 21:459–465 4724 314. Trüper HG, de’ Clari L (1997) Taxonomic note: erratum and correction of further specific 4725 epithets formed as substantives (nouns) “in apposition.” Int J Syst Bacteriol 48:615–615 4726 315. Spicher G, Schröder R (1978) Die Mikroflora des Sauerteiges, VI. Untersuchungen über die Art 4727 der in “Reinzuchtsauern” anzutreffenden Milchsäurebakterien. Genus Lactobacillus Beijerinck. 4728 Z Lebensm Unters Forsch 167:342–345 4729 316. Vogel RF, Pavlovic M, Ehrmann MA, Wiezer A, Liesegang H, Offschanka S, Voget S, Angelov A, 4730 Böcker G, Liebl W (2011) Genomic analysis reveals Lactobacillus sanfranciscensis as stable 4731 element in traditional sourdoughs. Microb Cell Fact 10:S6 4732 317. Gänzle MG, Ehmann M, Hammes WP (1998) Modeling of growth of Lactobacillus 4733 sanfranciscensis and Candida milleri in response to process parameters of sourdough 4734 fermentation. Appl Environ Microbiol 64:2616–2623 4735 318. Boiocchi F, Porcellato D, Limonta L, Picozzi C, Vigentini I, Locatelli DP, Foschino R (2017) Insect

122

4736 frass in stored cereal products as a potential source of Lactobacillus sanfranciscensis for 4737 sourdough ecosystem. J Appl Microbiol 123:944–955 4738 319. Hoang VA, Kim YJ, Nguyen NL, Kim SK, Yang DC (2015) Lactobacillus vespulae sp. nov., isolated 4739 from gut of a queen wasp (Vespula vulgaris). Int J Syst Evol Microbiol 65:3326–3332 4740 320. McFrederick QS, Thomas JM, Neff JL, Vuong HQ, Russell KA, Hale AR, Mueller UG (2017) 4741 Flowers and wild megachilid bees share microbes. Microb Ecol 73:188–200 4742 321. Edwards CG, Haag KM, Collins MD, Hutson RA, Huang YC (1998) Lactobacillus kunkeei sp. nov.: 4743 a spoilage organism associated with grape juice fermentations. J Appl Microbiol 84:698–702 4744 322. Chiou T‐Y, Suda W, Oshima K, Hattori M, Matsuzaki C, Yamamoto K, Takahashi T (2018) 4745 Lactobacillus kosoi sp. nov., a fructophilic species isolated from kôso, a Japanese sugar‐ 4746 vegetable fermented beverage. Antonie Van Leeuwenhoek 111:1149–1156 4747 323. Oren A, Garrity GM (2018) Validation List No. 183. List of new names and new combinations 4748 previously effectively, but not validly, published. Int J Syst Evol Microbiol 68:2707–2709 4749 324. McFrederick QS, Vuong HQ, Rothman JA (2018) Lactobacillus micheneri sp. nov., Lactobacillus 4750 timberlakei sp. nov. and Lactobacillus quenuiae sp. nov., lactic acid bacteria isolated from wild 4751 bees and flowers. Int J Syst Evol Microbiol 68:1879–1884 4752 325. Kawasaki S, Kurosawa K, Miyazaki M, Sakamoto M, Ohkuma M, Niimura Y (2011) Lactobacillus 4753 ozensis sp. nov., isolated from mountain flowers. Int J Syst Evol Microbiol 61:2435–2438 4754 326. Arena ME, Landete JM, Manca de Nadra MC, Pardo I, Ferrer S (2008) Factors affecting the 4755 production of putrescine from agmatine by Lactobacillus hilgardii X 1 B isolated from wine. J 4756 Appl Microbiol 105:158–165 4757 327. Lei X, Sun G, Xie J, Wei D (2013) Lactobacillus curieae sp. nov., isolated from stinky tofu brine. 4758 Int J Syst Evol Microbiol 63:2501–2505 4759 328. Krooneman J, Faber F, Alderkamp AC, Elferink SJ, Driehuis F, Cleenwerck I, Swings J, Gottschal 4760 JC, Vancanneyt M (2002) Lactobacillus diolivorans sp. nov., a 1,2‐propanediol‐degrading 4761 bacterium isolated from aerobically stable maize silage. Int J Syst Evol Microbiol 52:639–646 4762 329. Endo A, Okada S (2007) Lactobacillus farraginis sp. nov. and Lactobacillus parafarraginis sp. 4763 nov., heterofermentative lactobacilli isolated from a compost of distilled shochu residue. Int J 4764 Syst Evol Microbiol 57:708–712 4765 330. Douglas HC, Cruess W V. (1936) A Lactobacillus from California wine: Lactobacillus hilgardii. J 4766 Food Sci 1:113–119 4767 331. Vaughn RH, Douglas HC, Fornachon JCM (1949) The taxonomy of Lactobacillus hilgardii and 4768 related heterofermentative lactobacilli. Hilgardia 19:133–139 4769 332. Kandler O, Kunath P (1983) Lactobacillus kefir sp.nov., a component of the microflora of Kefir. 4770 Syst Appl Microbiol 4:286–294 4771 333. Watanabe K, Fujimoto J, Tomii Y, Sasamoto M, Makino H, Kudo Y, Okada S (2009) Lactobacillus 4772 kisonensis sp. nov., Lactobacillus otakiensis sp. nov., Lactobacillus rapi sp. nov. and 4773 Lactobacillus sunkii sp. nov., heterofermentative species isolated from sunki, a traditional 4774 Japanese pickle. Int J Syst Evol Microbiol 59:754–760 4775 334. Vancanneyt M, Engelbeen K, Wachter M De, Vandemeulebroecke K, Cleenwerck I, Swings J 4776 (2005) Reclassification of Lactobacillus ferintoshensis as a later heterotypic synonym of 4777 Lactobacillus parabuchneri. Int J Syst Evol Microbiol 55:2195–2198 4778 335. Bhandari RR, Walker TK (1953) Lactobacillus frigidus n.sp. isolated from brewery yeast. J Gen 4779 Microbiol 8:330–332

123

4780 336. Tanizawa Y, Kobayashi H, Kaminuma E, Sakamoto M, Ohkuma M, Nakamura Y, Arita M, Tohno 4781 M (2017) Genomic characterization reconfirms the taxonomic status of Lactobacillus 4782 parakefiri. Biosci Microbiota Food Heal 36:129–134 4783 337. Nicaise B, Maaloum M, Lo CI, Armstrong N, Bretelle F, Fournier P‐É, Diop K, Fenollar F (2019) 4784 Taxono‐genomics description of “Lactobacillus raoultii” sp. nov.’, strain Marseille‐P4006T, a 4785 new Lactobacillus species isolated from the female genital tract of a patient with bacterial 4786 vaginosis. New Microbes New Infect 29:100534 4787 338. Long GY, Wei YX, Tu W, Gu CT (2020) Lactobacillus hegangensis sp. nov., Lactobacillus 4788 suibinensis sp. nov., Lactobacillus daqingensis sp. nov., Lactobacillus yichunensis sp. nov., 4789 Lactobacillus mulanensis sp. nov., Lactobacillus achengensis sp. nov., Lactobacillus 4790 wuchangensis sp. nov., Lactobacillus gannanensis sp. nov., Lactobacillus binensis sp. nov. and 4791 Lactobacillus angrenensis sp. nov., isolated from Chinese traditional pickle and yogurt. Int J Syst 4792 Evol Microbiol doi: 10.1099/ijsem.0.004060 4793 339. Diaz M, Sayavedra L, Atter A, Mayer MJ, Saha S, Amoa‐Awua W, Narbad A (2020) Lactobacillus 4794 garii sp. nov., isolated from a fermented cassava product. Int J Syst Evol Microbiol 4795 10.1099/ijsem.0.004121 4796 340. Zhang Z, Wang Y, Hou Q, Zhao H, Li W, Sun Z, Guo Z (2020) Lactobacillus enshiensis sp. nov., a 4797 novel arsenic‐resistant bacterium. Int J Syst Evol Microbiol doi: 10.1099/ijsem.0.004072. 4798 4799

124

4800 FIGURES AND TABLES 4801 Figure 1. Cumulative number of species described in the genera Pediococcus and Lactobacillus until 4802 Jan. 2020. The species decribed in Jan. 2020 is included in the 2010 – 2019 count. 4803 Figure 2. Core genome phylogenetic tree of Lactobacillaceae. The phylogenomic analysis is based on 4804 the concatenated alignment of protein sequences for the 114 single‐copy core genes. The maximum 4805 likelihood tree was inferred by RAxML as described [14] using the 244 Lactobacillus and Pediococcus 4806 species for which genome sequence data was available on the NCBI database on August 19th, 2019. 4807 The tree was rooted via midpoint rooting. Bootstrap support values were calculated from 500 4808 replicates, and only values above 90% were labelled. Members of the same phylogenetic group that 4809 are the basis for the proposed taxonomy are indicated by the same color for branches, and the type 4810 strain of each group is printed in bold. Outer rings provide information on genomic features and the 4811 inferred lifestyle of the species. The color gradient in red represents the GC content of each genome 4812 sequence; higher GC contents are indicated by darker shading. The solid circles in brown represent 4813 genome sizes; the area of the circle correlates with the genome size. The second ring indicates the 4814 inferred natural habitats of the species as vertebrate host‐adapted (red), insect‐adapted (orange), 4815 nomadic (green), free‐living (blue) or unassigned (white). This assignment of species to lifestyle was 4816 based on [17]. 4817 Figure 3. Box plot of the intra‐family and inter‐family cAAI values in the families Leuconostocaceae 4818 and Lactobacillaceae. The reference line is drawn at a cAAI of 59% in both panels. 4819 Figure 4. Frequency distribution of pairwise cAAI in Lactobacillaceae and Leuconostocaceae. Inter‐ 4820 genus cAAI values are shown in descending order; Intra‐genus cAAI values are shown in ascending 4821 order for the current taxonomy (dotted lines) and for the proposed taxonomy that divides the genus 4822 Lactobacillus in 25 genera (solid lines). Genera are color coded; Lactobacillus; Pediococcus, 4823 Leuconostoc, and Weissella. The number of pairwise cAAI values that is represented by the lines is 4824 indicated in the figure legend. Owing to the low number of values, intra‐genus cAAI values for 4825 Fructobacillus, Oenococcus and Convivina are not shown. The data used for the graph is provided in 4826 online supplementary Table S3. 4827 Figure 5. Range of pairwise intra‐genus cAAI values for all current and proposed genera in the families 4828 Lactobacillaceae and Leuconostocaceae. The dotted line designates the lowest cAAI value for current 4829 genera excluding Lactobacillus. Bars and symbols are coloured gray if the genus is exclusive, i.e. if the 4830 lowest intra‐genus cAAI is higher than any inter‐genus cAAI of species in that genus. Bars and symbols 4831 are coloured red and green, respectively, if the genus is non‐exclusive, i.e. if the lowest intra‐genus 4832 cAAI is lower than the highest inter‐genus cAAI of species in that genus. Trivial values (100% for self 4833 to self comparison) are shown only for genera that include one species. The data used for the graph 4834 is provided in online supplementary Table S3. The y‐axis label uses the proposed taxonomy as follows 4835 Lentilactobacillus ‐ L. buchneri group; Secundilactobacillus ‐ L. collinoides group; Levilactobacillus ‐ L. 4836 brevis group; Fructilactobacillus ‐ L. fructivorans group; Acetilactobacillus, no prior designation; 4837 Apilactobacillus ‐ L. kunkeei group; Limosilactobacillus – L. reuteri group; Paucilactobacillus – L. 4838 vaccinostercus group; Furfurilactobacillus – L. rossiae group; Lactiplantibacillus – L. plantarum group; 4839 Ligilactobacillus – part of L. salivarius group; Liquorilactobacillus ‐ part of L. salivarius group; Dellaglioa 4840 – L. algidus; Loigolactobacillus – L. coryniformis group; Paralactobacillus – L. selangorensis; 4841 Latilactobacillus – L. sakei group; Lacticaseibacillus – L. casei group; Agrilactobacillus – L. composti; 4842 Schleiferilactobacillus – L. perolens group; Lapidilactobacillus – L. dextrinicus / convacus; 4843 Companilactobacillus – L. alimentarius group; Bombilactobacillus – L. mellifer / mellis group; 4844 Lactobacillus – L. delbrueckii group; Amylolactobacillus – L. amylophilus group; Holzapfelia – L. florum.

125

4845 Figure 6. Gene family presence/absence patterns in Lactobacillaceae and Leuconostocaceae. Each 4846 column represents a gene family presence/absence pattern in species of Lactobacillaceae and 4847 Leuconostoaceae, where presence is indicated with a dot. The absolute number of gene families that 4848 conform to each pattern is visualized in the marginal bar plot at the top. Separations between 4849 phylogroups are indicated with horizontal black lines. We defined genes that were present in all 4850 genomes of a clade and in none of the genomes outside of that clade as “signature genes” (dark blue); 4851 other genes are shown in light blue). Only presence/absence patterns followed by four or more gene 4852 families are shown. Patterns of presence in a single species or all species are not shown. Unassigned 4853 species are clusters of closely related genomes which could not be assigned to a known species due 4854 to low whole‐genome similarity to a type strain and / or low 16S rRNA similarity to a type strain. 4855 Figure 7. 4856 Panel (a). Core genome phylogenetic tree with the type strains of 25 phylogenetic groups of the genus 4857 Lactobacillus, 31 type strains of other genera in the Lactobacillales, and 8 type strains from Bacillales 4858 as outgroup. The phylogenomic analysis is based on the concatenated protein sequences of 170 single 4859 copy core genes. The maximum likelihood tree was inferred by RAxML as described (12). Bootstrap 4860 support values were calculated from 500 replicates, and only values of > 80% are labeled. Members 4861 of the same bacterial families are colour coded. 4862 Panel (b). Overview tree of phylogroups of Lactobacillaceae and Leuconostocaceae. Subtree of the 4863 tree shown in Figure S4; only the branches corresponding to type species of phylogroups of 4864 Lactobacillaceae or genera of Leuconostocaceae are shown. 4865 Figure 8. Heat map depicting the cAAI values of the 38782 pairwise comparisons of all species in the 4866 families Leuconostocaceae and Lactobacillaceae for which genome sequence data was available in 4867 August 2019. The source file is provided as Table S3.

126

250

200

150

100

Cumulative number of species of number Cumulative 50

0 1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 2010 2020 Decade of new description Tree scale: 0.1

Lifestyle

vertebrate host L. ginsenosidimutans

L. versmoldensis

L. mishanensis L. metriopterae

L. amylophilus

Insect host L. amylovorus L. floricola L. mellifer

L. mellis L. kitasatonis L. bombi

L. acidophilus L. ultunensis L. kefiranofaciens

L. helveticus L. gallinarum

Environmental L. furfuricola L. zhongbaensis L. keshanensis L. kedongensis L. tucceti L. baiquanensis L. hulinensis L. crispatus L. allii L. intestinalis L. insicii L. nodensis L. amylolyticus L. jidongensis L. hamsteri L. suantsaicola Nomadic L. alimentarius L. paralimentarius L. kalixensis L. kullabergensis L. kimchii L. bobalius L. kimbladii L. helsingborgensis L. farciminis L. melliventris L. futsaii L. formosensis L. crustorum L. musae L. panisapium L. heilongjiangensis L. nantensis L. bombicola L. apis L. acetotolerans L. zhachilii 54 L. nuruki L. gigeriorum L. mindensis L. kimchiensis L. delbrueckiiL. pasteurii L. concavus L. equicursoris L. dextrinicus L. bayanensis L. composti L. jensenii 38 67 L. yilanensis L. psittaci 25 L. perolens L. johnsonii L. taiwanensis L. harbinensis L. paragasseri L. shenzhenensis L. pantheris L. gasseri L. thailandensis L. rodentium L. songhuajiangensis L. hominis 88 L. sharpeae L. hulanensis L. iners L. saniviri L. brantae 80 L. paracasei L. rhamnosus L. casei L. chiayiensis L. camelliae L. jixianensis L. parakefiri L. nasuensis L. buchneri L. manihotivorans L. otakiensis L. porcinae L. kefiri L. selangorensis L. sunkii L. fuchuensis L. parabuchneri L. sakei

L. rapi L. curvatus L. kisonensis L. graminis L. diolivorans L. rennini L. coryniformis L. raoultii L. zhaoyuanensis L. farraginis L. bifermentans L. hilgardii L. iwatensis L. parafarraginis L. backii L. curieae 57 L. algidus L. senioris L. vini L. micheneri L. nagelii L. kosoi L. ghanensis L. timberlakei L. capillatus L. quenuiae L. sucicola L. apinorum L. uvarum L. kunkeei 38 L. aquaticus L. ozensis L. satsumensis 38 L. jinshani 47 L. oeni L. cacaonum L. sanfranciscensis L. lindneri L. hordei L. florum L. mali L. hyakitensis L. fructivorans L. salivarius L. mulengensis L. saerimneri L. cerevisiae L. ceti L. araffinosus

L. suantsaiihabitans 80 L. yonginensis L. aviarius L. brevis L. salitolerans

L. fujinensis 45 L. acidipiscis L. koreensis L. pobuzihii L. equi L. huananensis L. agilis L. paucivorans L. ruminis L. lindianensis L. apodemi L. fuyuanensis L. murinus L. parabrevis L. animalis L. hammesii P. inopinatus P. damnosus L. tangyuanensis P. cellicola L. zymae L. senmaizukei P. ethanolidurans P. argentinicus L. acidifarinae P. claussenii L. suantsaii P. lolii P. acidilactici L. namurensisL. spicheri P. stilesii P. pentosaceus L. bambusae L. xiangfangensis L. mixtipabuli L. plajomi L. silagincola L. modestisalitolerans L. silagei L. herbarum L. pentosus L. pentosiphilus L. similis L. plantarum L. odoratitofui L. paraplantarum L. fabifermentans L. nangangensis L. daoliensis L. collinoides L. pingfangensis L. oryzae L. dongliensis L. kimchicus L. songbeiensis L. mudanjiangensis L. paracollinoides L. daowaiensis L. siliginis L. rossiae L. oligofermentans L. nenjiangensis L. vaccinostercus L. suebicus L. gorillae L. wasatchensis L. hokkaidonensis L. gastricus L. kaifaensis

L. equigenerosi L. malefermentans L. oris L. fermentum

L. antri L. ingluviei

L. panis L. mucosae L. coleohominis L. secaliphilus L. pontis

L. reuteri

L. frumenti

L. vaginalis "L. timonensis" Pairwise cAAI (%) 100 50 60 70 80 90 Leuconostocaceae Intra-family (n=595) Lactobacillaceae Intra-family (n=29646) Lactobacillaceae vs. Lactobacillaceae Leuconostocaceae inter-family ( n=8541 ) 1.0

0.8 Leuconostoc (n=66) 0.6 Weissella (n=91) Pediococcus (n=45) 0.4 proposed 25 genera Lactobacillus (n=2057)

cumulative frequency [-] cumulative frequency Inter-genus Lactobacillus proposed 0.2 (n=26218) Intra-genus Lactobacillus current (n=34517) 0.0

60 70 80 90 100 % cAmino Acid Identity of pairwise comparisons Weissella Oenococcus Convivina Fructobacillus Leuconostoc Lentilactobacillus Secundilactobacillus Levilactobacillus Fructilactobacillus Acetilactobacillus Apilactobacillus Limosilactobacillus Paucilactobacillus Furfurilactobacillus Lactiplantibacillus Pediococcus Ligilactobacillus Liquorilactobacillus Dellaglioa Loigolactobacillus Paralactobacillus Latilactobacillus Lacticaseibacillus Agrilactobacillus Schleiferilactobacillus Lapidilactobacillus Companilactobacillus Bombilactobacillus Lactobacillus Amylolactobacillus Holzapfelia

70 80 90 100 Pairwise intra-genus cAAI (%) 75

50

25

0

Lactobacillus buchneri ● ● ● ●● ● ● ●●● ● ●● ● ● Lactobacillus parakefiri ● ● ● ●● ●●● ●● ● Lactobacillus otakiensis ● ● ● ●● ● ●●● ● ●● ● Lactobacillus sunkii ● ● ● ● ●● ● ● ●●● ● ●● ● ● Lactobacillus kefiri ● ● ● ● ●● ● ●●● ●● ● Lactobacillus parabuchneri ● ● ● ●● ● ●●● ●● ● Lactobacillus kisonensis ● ● ● ● ● ● ● ● ●●● ● ● ● ●● ● Lactobacillus rapi ● ● ● ● ● ●● ● ●●● ●● ● ● ●● ● Lactobacillus diolivorans ● ● ● ● ●● ● ● ● ●●● ● ● ●● ●● ● ● Lactobacillus farraginis ● ● ● ● ● ●● ● ●● ● ● ●●● ●● ● ●● ● ● Lactobacillus raoultii ● ● ● ● ● ● ●● ● ● ●●● ● ● ●● ● ● Lactobacillus hilgardii ● ● ● ● ● ●● ● ●● ● ●●● ● ●● ● ● Lactobacillus parafarraginis ● ● ● ● ●● ● ● ● ●●● ● ●● ● Unassig. species 1 ● ● ●● ● ●●● ●● Lactobacillus curieae ● ● ●● ●●● ● ● Lactobacillus senioris ● ● ● ● ●●● ● Lactobacillus kunkeei ● ● ● ● ● ● ● ●●● ● ● Unassig. species 5 ● ● ● ● ● ● ● ●●● ● Lactobacillus apinorum ● ● ● ● ● ● ● ●●● ● ● Unassig. species 11 ● ● ● ● ● ●● ● Lactobacillus timberlakei ● ● ● ● ● ● ● ● ●●● ● ● Lactobacillus quenuiae ● ● ● ● ● ● ●●● ● ● Lactobacillus ozensis ● ● ● ● ● ● ●●● ● Lactobacillus sanfranciscensis ● ● ● ● ● ● ● Lactobacillus lindneri ● ● ● ● ● ● ● ● ● Lactobacillus florum ● ● ● ● ● ● Lactobacillus fructivorans ● ● ● ● ● ● ● ● Unassig. species 2 ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● Lactobacillus brevis ● ● ● ● ● ● ● ● ●●● ● ● ● Lactobacillus koreensis ● ● ● ● ● ● ● ● ●●● ● ● Lactobacillus parabrevis ● ● ● ● ● ● ●●● Lactobacillus hammesii ● ● ● ● ● ● ● ●●● ● ● Lactobacillus paucivorans ● ● ● ● ● ●●● ● Lactobacillus senmaizukei ● ● ● ● ● ● ● ● ●●● ● Lactobacillus spicheri ● ● ● ● ● ● ● ● ● ● ●●● ●● Lactobacillus namurensis ● ● ● ● ● ● ● ● ●●● ● Lactobacillus zymae ● ● ● ● ● ● ● ● ● ● ●●● ●● ● Lactobacillus acidifarinae ● ● ● ● ●● ● ● ● ● ●●● ●● ● Lactobacillus bambusae ● ●● ● ● ●●● ● Lactobacillus mixtipabuli ● ● ● ● ●● ● ●●●● ● Lactobacillus silagincola ● ● ● ● ●● ● ● ●●●● ● ● ● ● Lactobacillus pentosiphilus ● ● ●● ●● ● ●●● ● ● Lactobacillus silagei ● ● ● ● ●● ● ● ●●● ● ● ● ● Lactobacillus odoratitofui ● ● ● ● ● ●● ● ●●● ● Lactobacillus similis ● ● ● ● ● ●● ● ● ●●● ● ● ● ● ● Lactobacillus paracollinoides ● ● ● ● ● ●● ● ● ●●● ● ● Lactobacillus collinoides ● ● ● ● ● ● ●● ● ● ● ●●● ●● ● ● ● ● Lactobacillus kimchicus ● ● ● ● ● ● ●● ● ●●● ●● Lactobacillus malefermentans ● ● ● ● ●●● ● Lactobacillus oryzae ● ● ● ● ●●● ● Lactobacillus plantarum ● ● ● ● ●● ● ● ● ●● ● ●●● ● Lactobacillus paraplantarum ● ● ● ● ●● ●● ● ● ●● ● ●●● ● Lactobacillus pentosus ● ● ● ●● ● ● ● ●● ● ● ●●● ● ● Lactobacillus herbarum ● ● ● ● ●● ● ● ●● ● ●●● ● Lactobacillus xiangfangensis ● ● ● ● ● ●● ● ● ●●● ● Unassig. species 8 ● ● ● ●● ● ●● ● ●●● ● ● ● Unassig. species 9 ● ● ● ● ● ●● ●●● ● ● ● Lactobacillus fabifermentans ● ● ● ● ● ● ●● ● ●●● ● ●● ● ● ● ● ● ● ●● ●●● Leuconostoc lactis ● ● ● ● ● ● ● ● ● ● ●●● ● Leuconostoc kimchii ●● ● ● ● ●● ● ● ●●● ● ● ● ● ● ● ● ● ●● ● ● ●●● ● ● ● ● ● ●● ● ● ●●● ● Leuconostoc mesenteroides ● ● ● ●● ● ●●● ● ● ● Leuconostoc pseudomesenteroides ●● ● ● ● ● ●● ● ●● ●●● ● ● Leuconostoc fallax ● ● ● ● ●● ●●● Fructobacillus tropaeoli ● ● ● ● ● ● ● ●● ● ●●● ● Fructobacillus pseudoficulneus ● ● ● ● ● ● ●●● Fructobacillus ficulneus ● ● ● ● ● ● ●● ●●● ● Fructobacillus fructosus ● ● ● ● ● ● ●●● ● Fructobacillus durionis ● ● ● ● ● ●●● ● Convivina intestini ● ● ●● ●●● ● ● ● ●●● Oenococcus kitaharae ● ●● ●●● ● ● ●● ● ● ● ● ●●● ● Unassig. species 14 ● ●● ● ● ● ● ●●● Unassig. species 13 ● ●● ● ● ● ● ●●● ● Weissella paramesenteroides ● ●● ● ● ● ●●● Weissella thailandensis ● ●● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ●●● Weissella confusa ● ● ● ● ● ● ●●● ● Weissella halotolerans ● ● ● ●●● Weissella ceti ● ● ● ● ● ●●● Weissella viridescens ● ● ● ● ● ●●● ● Weissella minor ● ● ● ● ● ●●● ● ● ● ● ● ● ●● ● ● ● ● ● ●● Weissella kandleri ● ● ● ● ●● ● Weissella soli ● ● ● ● ●●● ● Lactobacillus rossiae ● ● ● ● ● ● ● ● ●●● ● Lactobacillus siliginis ● ● ● ● ● ● ●●● ● Lactobacillus antri ● ● ● ● ● ● ● ● ●● ● ● Lactobacillus oris ● ● ● ● ● ● ● ● ● ●● ● Lactobacillus panis ● ● ● ● ● ● ● Lactobacillus pontis ● ● ● ● ● ●● Unassig. species 7 ● ● ● ● ● ●● Lactobacillus reuteri ● ● ● ● ● ●● Unassig. species 16 ● ● ● ● ● ● ● ● ●● ● Lactobacillus vaginalis ● ● ● ● ●● ● ● Lactobacillus frumenti ● ● ● ● ● ● ● Lactobacillus fermentum ● ● ● ● ●● ●● ● Lactobacillus gorillae ● ● ● ● ● ●● Lactobacillus gastricus ● ● ●● ●● ● ● Lactobacillus equigenerosi ● ● ● ● ●● ● Lactobacillus coleohominis ● ● ● ●●● ● Lactobacillus secaliphilus ● ● ● ●● Lactobacillus ingluviei ● ● ● ●●● ● ● Lactobacillus mucosae ● ● ● ●● ●● ● ● 'Lactobacillus timonensis' ● ● ● ● ● Lactobacillus suebicus ● ● ● ● ●● ●● ● ● Lactobacillus vaccinostercus ● ● ● ● ●● ●● ● Lactobacillus hokkaidonensis ● ● ● ● ●● ● ●● Lactobacillus wasatchensis ● ● ● ● ● ●● ● Lactobacillus oligofermentans ● ● ● ● ●● Pediococcus pentosaceus ● ● ● ● ● ● ● ●●● ● Pediococcus stilesii ● ● ● ● ● ● ● ●●● Pediococcus acidilactici ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●●● ● Pediococcus argentinicus ● ● ● ● ● ● ●●● Pediococcus ethanolidurans ● ● ● ● ●● ● ●●● ● Pediococcus parvulus ● ● ● ● ● ● ● ●●● ● ● ● Pediococcus cellicola ● ● ● ● ●● ● ● ●●● ● ● ● ● ● ● ● ●●● ● ● Pediococcus inopinatus ● ● ● ● ● ●●● Lactobacillus murinus ● ● ● ● ● ● ● ● ● ●●● ● Lactobacillus animalis ● ● ● ● ● ● ●●● Lactobacillus apodemi ● ● ● ● ● ● ●●● Lactobacillus ruminis ● ● ● ● ● ●● ● ●●● ● Unassig. species 15 ● ● ● ● ● ●●● ● ● Lactobacillus equi ● ● ● ● ● ●●● ● ● Lactobacillus agilis ● ● ● ● ● ●● ●●● ● Lactobacillus pobuzihii ● ● ● ● ● ●●● ● Lactobacillus acidipiscis ● ● ● ● ● ●●● ● Lactobacillus araffinosus ● ● ● ● ● ●● Lactobacillus aviarius ● ● ● ● ●● Lactobacillus salivarius ● ● ●● ● ●●● ● ● Lactobacillus hayakitensis ● ● ● ● ● ●●● Lactobacillus ceti ● ● ● ●● ● Lactobacillus saerimneri ● ● ● ● ●●● Lactobacillus hordei ●● ● ● ● ●● ● ●●● ● Lactobacillus mali ●● ● ● ● ● ●● ●●● ● ● ● Lactobacillus cacaonum ● ● ● ●● ●●● ● ● ● Lactobacillus satsumensis ● ● ●● ● ●● ● ●●● ● ● ● Lactobacillus oeni ● ● ● ● ●● ●●● ● ● ● ● Lactobacillus uvarum ● ● ● ● ●● ● ● ●●● ● ● ● Lactobacillus aquaticus ● ● ● ● ● ●● ● ●●● ● ● Lactobacillus sucicola ● ● ● ● ● ●● ●●● ● ● ● ●● Lactobacillus capillatus ● ● ● ● ● ●● ●●● ● ● ●● Lactobacillus nagelii ● ● ● ● ●● ●● ● ●●● ● ● Lactobacillus ghanensis ● ● ● ● ●● ●● ● ●●● ● ●● Lactobacillus vini ● ● ● ● ●● ●●● ● ● Lactobacillus algidus ● ● ● ●●● Lactobacillus kimbladii ● ● ● ● ● ●●● ● ● ● ● Lactobacillus kullabergensis ● ● ● ● ● ● ●●● ● ● Lactobacillus melliventris ● ● ● ● ● ● ● ●●● ● ● ● Lactobacillus helsingborgensis ● ● ● ● ●●● ● ● ● Lactobacillus bombicola ● ● ● ● ● ●●● ●●● ● ● ● ● ● ● Unassig. species 12 ● ● ● ● ●●● ●● ● ● ● ● ● Lactobacillus panisapium ● ● ● ● ●●● ● ● Lactobacillus apis ● ● ● ● ● ● ●●● ● ● Lactobacillus acetotolerans ● ● ● ● ●●● ● ● Lactobacillus amylovorus ● ● ● ● ● ● ●●● ● ● ● ● ● Lactobacillus kitasatonis ● ● ● ● ● ● ●●● ● ● Lactobacillus ultunensis ● ● ● ● ● ● ● ●●● ● Lactobacillus kefiranofaciens ● ● ● ● ● ● ●●● ● ● ● Lactobacillus helveticus ● ● ● ● ● ● ●●● ● ● ● Lactobacillus gallinarum ● ● ● ● ● ●●● ● Lactobacillus acidophilus ● ● ● ● ● ●●● ● Lactobacillus crispatus ● ● ● ● ● ●●● ● ● ● Lactobacillus intestinalis ● ● ● ● ●●● ● ● Lactobacillus amylolyticus ● ● ● ● ●●● ● Lactobacillus kalixensis ● ● ● ● ● ●●● ● Lactobacillus hamsteri ● ● ● ● ● ●●● ● ● ● Unassig. species 6 ● ● ● ● ● ● ● ●●● ●● ● ● ● ● ● ● Lactobacillus gigeriorum ● ● ● ● ● ● ● ●●● ● Lactobacillus pasteurii ● ● ● ● ● ●●● ● ● Lactobacillus delbrueckii ● ● ● ● ● ● ● ●●● ● ● Lactobacillus equicursoris ● ● ● ● ●● ● ● ● ●●● ● ● Unassig. species 3 ● ● ● ● ●● ● ● ●●● ● ● Unassig. species 4 ● ● ● ● ● ● ●●● ● Lactobacillus jensenii ● ● ● ● ● ● ●●● ● ● Lactobacillus psittaci ● ● ● ● ● ●●● ● Lactobacillus gasseri ● ● ● ● ● ● ● ●●● ● ● Lactobacillus taiwanensis ● ● ● ● ● ● ● ●●● ● ● Lactobacillus johnsonii ● ● ● ● ● ● ● ● ●●● ● ● ● Lactobacillus hominis ● ● ● ● ● ● ● ●●● ● ● ● Lactobacillus rodentium ● ● ● ● ● ● ● ●●● ● Lactobacillus iners ● ● ● ● ●●● ● ● Lactobacillus amylophilus ● ● ● ● ●●● ● Lactobacillus floricola ● ● ● ● ●●● Lactobacillus nantensis ● ● ● ● ● ● ● ● ● ● ●●● ● Unassig. species 10 ● ● ● ● ● ● ● ● ● ●●● Lactobacillus heilongjiangensis ● ● ● ● ● ● ● ● ●●● Lactobacillus mindensis ● ● ● ● ● ● ●●● Lactobacillus kimchiensis ● ● ● ● ● ● ● ● ●●● Lactobacillus nuruki ● ● ● ● ● ● ● ●●● Lactobacillus crustorum ● ● ● ● ● ● ●●● Lactobacillus musae ● ● ● ● ● ● ● ● ●●● Lactobacillus formosensis ● ● ● ● ● ● ●● ●●● Lactobacillus futsaii ● ● ● ● ● ● ● ●● ● ●●● ● Lactobacillus farciminis ● ● ● ● ● ● ● ●● ● ●●● ● Lactobacillus paralimentarius ● ● ● ●● ● ● ● ●●● ● Lactobacillus kimchii ● ● ● ● ●● ● ● ●●● ● Lactobacillus alimentarius ● ● ● ● ● ● ● ●●● Lactobacillus nodensis ● ● ● ● ● ● ● ● ●● ● ●●● ● ● ● Lactobacillus allii ● ● ● ● ● ● ● ● ● ● ●● ●● ●●● ● ● Lactobacillus tucceti ● ● ● ● ● ● ● ●● ●● ● ●●● ● Lactobacillus ginsenosidimutans ● ● ● ● ● ● ● ●● ● ● ● ●●● ● ● ● ● ● Lactobacillus versmoldensis ● ● ● ● ● ● ● ● ● ●● ●● ● ●●● ● ● ● Lactobacillus metriopterae ● ● ● ● ● ● ●●● ● Lactobacillus mellis ● ● ● ● ● ● ●●● ● Lactobacillus bombi ● ● ● ● ● ● ● ●●● Lactobacillus mellifer ● ● ● ● ● ●● ●●● ● ● Lactobacillus concavus ●● ● ● ●●●● Lactobacillus dextrinicus ●● ● ● ● ●●●● Lactobacillus shenzhenensis ● ● ● ● ● ● ● ●●●● ● ● Lactobacillus harbinensis ● ● ● ● ● ● ● ●●●● ● ● Lactobacillus perolens ● ● ● ● ● ● ● ●●●● ● Lactobacillus composti ● ● ● ● ● ● ● ●● ● ● ● ● ●●●● ● ●● ● ● ● Lactobacillus rhamnosus ● ●● ● ● ●● ●● ● ●●●● ●● ● Lactobacillus casei ● ● ● ● ● ● ●● ●●●● ● ● Lactobacillus paracasei ● ● ● ● ● ● ●● ● ●●●● ●● ● Lactobacillus nasuensis ● ● ● ● ● ● ●●●● ● Lactobacillus manihotivorans ● ● ● ● ● ● ●● ● ●●●● ● ● Lactobacillus camelliae ● ● ● ● ● ●●●● ● ● ● ● ● Lactobacillus brantae ● ● ● ● ● ●●●●● ● Lactobacillus saniviri ● ● ● ●● ● ● ● ●●●● ● ● Lactobacillus pantheris ● ● ● ● ● ●●●● Lactobacillus thailandensis ● ● ● ● ● ●●●●● ● Lactobacillus sharpeae ● ● ● ● ● ● ●●●● ● Lactobacillus curvatus ● ● ● ● ●●●●● ● ● Lactobacillus graminis ● ● ● ● ● ● ●●●● ● Lactobacillus sakei ● ● ● ● ●●●● ● Lactobacillus fuchuensis ● ● ● ● ● ●●●● ● ● ● ● Lactobacillus selangorensis ● ● ● ● ●●●● ● Lactobacillus coryniformis ● ● ● ● ● ● ● ● ●● ● ● ● ●●●● ● ●● ● Lactobacillus rennini ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●●● ● ● Lactobacillus bifermentans ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ●●●● ● ● Lactobacillus backii ● ● ● ● ● ● ● ●● ● ● ● ●● ● ● ● (a) (b)

A taxonomic note on the genus Lactobacillus: Description of 24 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

Jinshui Zheng1,$, Stijn Wittouck2,$, Elisa Salvetti3, $, Charles M.A.P. Franz4, Hugh M.B. Harris5, Paola Mattarelli6, Paul O’Toole5, Bruno Pot7, Peter Vandamme8, Jens Walter9, 10, Koichi Watanabe11, 12, Sander Wuyts2, Giovanna E. Felis3, #*, Michael G. Gänzle9, 13#*, Sarah Lebeer2 #

Online supplementary figures and tables.

Table S1. List of species and subspecies of Lactobacillaceae and Leuconostocaceae that were included in analyses. Lister are the type strains, the lifestyle of the organisms, accession numbers for genome sequence data and 16S rRNA sequence data, and the proposed new taxonomic position.

The file listing all species in the Lactobacillaceae is also available on https://site.unibo.it/subcommittee‐ lactobacillus‐bifidobacterium/en; the file hosted on the website will be periodically updated by adding new species that have been validly published.

Table S2. Genomes used for the iqtree phylogenetic analysis and the gene presence/absence analyses.

Table S3. Pairwise comparison of cAAI values of species in the Lactobacillaceae and Leuconostocaceae.

Table S4. Pairwise comparison of AAI values of species in the Lactobacillaceae and Leuconostocaceae.

Table S5. Signature genes and number of species of phylogroups.

Figure S1. Box plot of intra‐family and inter‐family AAI values in the families Leuconostocaceae and Lactobacillaceae.

Figure S2. Frequency distribution of pairwise amino acid identity (AAI) in Lactobacillaceae and Leuconostocaceae.

Figure S3. Range of pairwise intra‐genus amino acid identity (AAI) values for all proposed genera in the families Lactobacillaceae and Leuconostocaceae.

Figure S4. Full phylogenetic species tree of Lactobacillaceae, Leuconostocaceae and outgroups. The figure is provided as separate image file.

Figure S5. Core genome phylogenetic tree of Lactobacillaceae and Leuconostococaceae. The figure is provided as separate image file.

Figure S6. Phylogenetic tree on the basis of 16S rRNA gene sequences of the proposed species of Lactobacillaceae with three or more species.

Figure S7. Top amino acid identity (AAI) values of genomes to genera.

100

90

80

70 Pairwise AAI (%) (%) AAI Pairwise

60

50

Intra-family Intra-family inter-family Leuconostocaceae Lactobacillaceae Lactobacillaceae vs. (n=465) (n=22790) Leuconostocaceae (n=6634)

Figure S1. Box plot of intra‐family and inter‐family AAI values in the families Leuconostocaceae and Lactobacillaceae. The analysis was performed with genome sequence data that was available in May 2019. The reference line is drawn at an AAI of 56%. 1.0

0.8

Leuconostoc 0.6 (n=55) Weissella (n=91) 0.4 Pediococcus (n=55) 24 genera Lactobacillus kumulative frequency [-] (n=1631) 0.2 Inter-genus (n=28174) old genus Lactobacillus 0.0 (n=20503) 50 60 70 80 90 100 110

% Amino Acid Identity of pairwise comparisons Figure S2. Frequency distribution of pairwise amino acid identity (AAI) in Lactobacillaceae and Leuconostocaceae. Inter‐genus AAI values are shown in descending order; Intra‐genus AAI values are shown in ascending order for the current taxonomy (dotted lines) and for the proposed taxonomy that divides the genus Lactobacillus in 24 genera (solid lines). All genomes that were available in May 2019 were used for the analysis, excluding L. jinshani (proposed genus Acetilactobacillus). Genera are color coded; Lactobacillus; Pediococcus, Leuconostoc, and Weissella. The number of pairwise AAI values that is represented by the lines is indicated in the figure legend. Owing to the low number of values, intra‐genus AAI values for Fructobacillus, Oenococcus and Convivina are not shown. The data used for the graph is provided in online supplementary Table S4. Weissella Oenococcus Convivina Fructobacillus Leuconostoc Lentilactobacillus Secundilactobacillus Levilactobacillus Fructilactobacillus Apilactobacillus Limosilactobacillus Paucilactobacillus Furfurilactobacillus Lactiplantibacillus Pediococcus Ligilactobacillus Liquorilactobacillus Dellaglioa Loigolactobacillus Paralactobacillus Latilactobacillus Lacticaseibacillus Agrilactobacillus Schleiferilactobacillus Lapidilactobacillus Companilactobacillus Bombilactobacillus Lactobacillus Amylolactobacillus Holzapfelia

60 70 80 90 100 Pairwise intra-genus AAI (%)

Figure S3. Range of pairwise intra‐genus amino acid identity (AAI) values for all proposed genera in the families Lactobacillaceae and Leuconostocaceae. The dotted line designates the lowest AAI value for current genera excluding Lactobacillus. Bars and symbols are coloured gray if the genus is exclusive, i.e. if the lowest intra‐genus AAI is higher than any inter‐genus AAI of species in that genus. Bars and symbols are coloured red and green, respectively, if the genus is non‐exclusive, i.e. if the lowest intra‐genus AAI is lower than the highest intra‐genus AAI of species in that genus. All genomes that were available in May 2019 were used for the analysis, excluding L. jinshani (proposed genus Acetilactobacillus). The data used for the graph is provided in online supplementary Table S3.

Lactobacillus ginsenosidimutans

Lactobacillus shenzhenensis

Lactobacillus versmoldensis Lactobacillus concavus Lactobacillus harbinensis Lactobacillus metriopterae

Lactobacillus dextrinicus LactobacillusLactobacillus paralimentarius alimentarius Lactobacillus mellifer

Lactobacillus nodensis Lactobacillus bombiLactobacillus mellis

Lactobacillus formosensis Lactobacillus tucceti Lactobacillus farciminis

Lactobacillus kimchii Lactobacillus heilongjiangensisLactobacillus crustorum Lactobacillus allii

LactobacillusLactobacillus kimchiensis mindensisLactobacillus futsaii Lactobacillus musae Lactobacillus nuruki Lactobacillus Lactobacillusamylophilus nantensis Lactobacillus floricola Unassig. species 10

Lactobacillus perolens Lactobacillus composti Lactobacillus manihotivorans Lactobacillus nasuensis Lactobacillus camelliae Lactobacillus casei Lactobacillus rhamnosus Lactobacillus paracasei Lactobacillus saniviri Lactobacillus brantae Lactobacillus rodentium Lactobacillus thailandensis Lactobacillus hominis Lactobacillus pantheris Lactobacillus iners Lactobacillus sharpeae Lactobacillus graminis Lactobacillus curvatus Lactobacillus johnsonii Lactobacillus sakei Lactobacillus taiwanensis Lactobacillus fuchuensis Lactobacillus selangorensis Lactobacillus backii Lactobacillus gasseri Lactobacillus bifermentans Lactobacillus rennini Lactobacillus coryniformis Tetragenococcus halophilus Lactobacillus psittaci Enterococcus_F saccharolyticus Enterococcus_I aquimarinus Enterococcus_E cecorum LactobacillusLactobacillusUnassig. delbrueckii jenseniispecies 4 Enterococcus_G sulfureus Enterococcus_D sp001297065 Lactobacillus equicursoris Enterococcus_C dispar Unassig. species 3 Enterococcus_A raffinosus Enterococcus_B faecium_B Lactobacillus gigeriorum Enterococcus faecalis Melissococcus plutonius LactobacillusLactobacillus amylolyticus pasteurii Enterococcus_H canis Enterococcus_J timonensis Floricoccus penangensis Lactobacillus kalixensis agalactiae Lactobacillus hamsteri Pilibacter termitis Lactobacillus intestinalis Vagococcus fluvialis Unassig. species 6 86 Vagococcus_A lutrae Lactobacillus crispatus Catellicoccus marimammalium Lactobacillus acidophilus ruoffiae Facklamia_B sourekii Lactobacillus helveticus coleocola Lactobacillus gallinarum Facklamia_A sp003521095 Lactobacillus kefiranofaciens Facklamia hominis Globicatella sulfidifaciens Lactobacillus ultunensis Abiotrophia defectiva Lactobacillus amylovorus Dolosicoccus paucivorans Lactobacillus kitasatonis Aerococcus urinae_D Lactobacillus acetotolerans Atopobacter phocae Lactobacillus helsingborgensis 81 83 Bavariicoccus seileri 87 Granulicatella balaenopterae 59 81 Trichococcus flocculiformis Lactobacillus melliventris Jeotgalibaca sp001975685 Lactobacillus kimbladii Atopostipes suicloacalis Lactobacillus kullabergensis 49 Allofustis seminis Alloiococcus otitis Lactobacillus bombicola Dolosigranulum pigrum Unassig. species 12 Marinilactibacillus piezotolerans_A Lactobacillus panisapium Alkalibacterium subtropicum Atopococcus tabaci Lactobacillus apis Lacticigenium naphtae Lactobacillus algidus incerta Pisciglobus halotolerans Lactobacillus vini Carnobacterium_A jeotgali Lactobacillus nagelii Isobaculum melis Lactobacillus ghanensis Carnobacterium maltaromaticum Lactobacillus capillatus Lactobacillus sucicola 69 Listeria_A newyorkensis Lactobacillus uvarum Brochothrix thermosphacta Lactobacillus parakefiri Lactobacillus aquaticus Lactobacillus buchneri Lactobacillus satsumensis Lactobacillus otakiensis Lactobacillus oeni Lactobacillus kefiri Lactobacillus sunkii Lactobacillus cacaonum Lactobacillus parabuchneri Lactobacillus hordei Lactobacillus rapi Lactobacillus mali Lactobacillus kisonensis Lactobacillus ceti 86 Lactobacillus diolivorans Lactobacillus raoultii Lactobacillus saerimneri Lactobacillus farraginis Lactobacillus salivarius Lactobacillus hilgardii Lactobacillus hayakitensis Lactobacillus parafarraginis Lactobacillus pobuzihii Unassig. species 1 Lactobacillus curieae Lactobacillus acidipiscis Lactobacillus senioris Lactobacillus araffinosus Unassig. species 5 Lactobacillus aviarius Lactobacillus kunkeei Lactobacillus equi Lactobacillus apinorum Lactobacillus agilis Unassig. species 11 Lactobacillus quenuiae Lactobacillus ruminis Lactobacillus timberlakei Unassig. species 15 Lactobacillus ozensis Lactobacillus lindneri Lactobacillus apodemi Lactobacillus sanfranciscensis Lactobacillus murinus Lactobacillus florum Lactobacillus animalis 65 Lactobacillus fructivorans Lactobacillus hammesii Pediococcus claussenii Lactobacillus parabrevis Lactobacillus paucivorans Pediococcus argentinicus Lactobacillus brevis Unassig. species 2 PediococcusPediococcus acidilactici stilesii Lactobacillus koreensis Pediococcus pentosaceus Lactobacillus senmaizukei Lactobacillus acidifarinae Pediococcus damnosus Lactobacillus zymae Lactobacillus namurensis PediococcusPediococcus inopinatus cellicola Lactobacillus spicheri Lactobacillus bambusae Lactobacillus silagincola Lactobacillus mixtipabuli Pediococcus parvulus Lactobacillus pentosiphilus Pediococcus ethanolidurans Lactobacillus silagei Lactobacillus odoratitofui Lactobacillus suebicus Lactobacillus similis Lactobacillus collinoides Lactobacillus paracollinoides Lactobacillus oligofermentans Lactobacillus kimchicus Lactobacillus oryzae Lactobacillus malefermentans Lactobacillus paraplantarum Lactobacillus plantarum Lactobacillus vaginalis Lactobacillus pentosus LactobacillusLactobacillus vaccinostercus hokkaidonensisLactobacillus frumenti Lactobacillus herbarum Lactobacillus wasatchensisLactobacillus reuteri Lactobacillus xiangfangensis Unassig. species 9 Unassig. species 16 Unassig. species 8 Lactobacillus fabifermentans Lactobacillus pontis Leuconostoc gelidum Unassig. species 7 Leuconostoc kimchii Leuconostoc lactis Leuconostoc citreum Leuconostoc carnosum Lactobacillus panis Leuconostoc pseudomesenteroides Lactobacillus antri Leuconostoc mesenteroides Leuconostoc fallax Fructobacillus pseudoficulneus Lactobacillus oris Fructobacillus tropaeoli Fructobacillus ficulneus Fructobacillus durionis Fructobacillus fructosus Convivina intestini Oenococcus kitaharae

Lactobacillus mucosae 'LactobacillusLactobacillus timonensis' ingluviei Weissella soli

Lactobacillus gorillae Weissella ceti LactobacillusLactobacillus coleohominis secaliphilus Lactobacillus gastricus Weissella oryzae Weissella kandleri Lactobacillus siliginis Weissella minor Lactobacillus fermentum Weissella koreensis Lactobacillus rossiae Weissella cibaria

Lactobacillus equigenerosi Weissella confusa

Oenococcus oeni Weissella halotolerans Weissella hellenica

Unassig. species 13

Unassig. species 14 Weissella viridescens

Weissella thailandensis

Weissella paramesenteroides Figure S4. Full phylogenetic species tree of Lactobacillaceae, Leuconostocaceae and outgroups. The tree was inferred on a protein supermatrix of 294 single-copy core genes, all of which were present in a single copy in at least 99% of the genomes. Bootstrap support values were calculated based on 1000 replicates; only support values of less than 90% are shown. Labels are colored according to the family of the species; light blue for Lactobacillaceae, dark blue for Leuconostocaceae and light green for the outgroup species (one for each genus of the order Lactobacillales). Type species of phylogroups are shown in bold.

Figure S5. Core genome phylogenetic tree of Lactobacillaceae and Leuconostococaceae. The phylogenomic analysis is based on the concatenated protein sequences of 101 single-copy core genes. The maximum likelihood tree was inferred by RAxML as described (12) using the 297 species for which genome sequence data was available on the NCBI database in August, 2019. All nodes have more than 92% bootstrap support. Members of the same phylogenetic group are indicated by the same color for branches, and the type strain of each group is printed in bold. Outer rings provide information on genomic features and the lifestyle of the species. The color gradient in red represents the GC content of each genome sequence; higher GC contents are indicated by darker shading. The solid circles in brown represent genome sizes; the area of the circle correlates with the genome size. The second ring indicates the natural habitats of the species as vertebrate host-adapted (red), insect-adapted (orange), nomadic (green), environmental (blue) or unassigned (white). The assignment of species to lifestyle was based on (11). Fig. S6A Fig. S6B

Fig. S6C Fig. S6D

Fig. S6E

Fig. S6F Fig. S6G

Fig. S6H

Fig. S6I Fig. S6J

Fig. S6K Fig. S6L

Fig. S6M

Fig. S6N Fig. S6O

Fig. S6P Fig. S6Q

Fig. S6R

Fig. S6S Figure S6. Phylogenetic tree on the basis of 16S rRNA gene sequences of the proposed species of Lactobacillaceae with three or more species. Holzapfelia floricola was used as outgroup for all trees. The Figure includes all species that were effectively or validly published species as of Dec. 12th, 2019. Shown are the following proposed genera: Panel A, emended genus Lactobacillus; Panel B, Bombilactobacillus; Panel C, Companilactobacillus; Panel D, Lapidilactobacillus; Panel E, Schleiferilactobacillus; Panel F, Lacticaseibacillus; Panel G, Latilactobacillus; Panel H, Loigolactobacillus; Panel I, Liquorilactobacillus; Panel J, Ligilactobacillus; Panel K, Lactiplantibacillus; Panel L, Furfurilactobacillus; Panel M, Paucilactobacillus; Panel N, Limosilactobacillus; Panel O, Secundilactobacillus; Panel P, Levilactobacillus; Panel Q, Fructilactobacillus; Panel R, Apilactobacillus; Panel S, Lentilactobacillus.

● ●● ●●● ●●● ● ● ●●● ●●● ●● ●● ● ● ● ● ● ● ● ●●● ●●● ●●● ● ●● ●●●● ●●● ●●● ● ● ● ●● ●● ● ●●● ●●●● ● ●●●●● ● ● ● ● ● ● ●●● ●●● ●● ●●● ●● ● ●●● ●● ● ● ● ● ● ● ● ●●●● ●● ● ● ●●●● ●●● ●●●● ● ● ● ● ● ●●● ●●● ● ● ●●●● ● ●●●●● ● ● ● ● ● ● ● ● ●●● ● ●●● ●●●●●●● ●● ●●● ● ● ● ● ● ●● ●● ●● ●● ●● ●●●● ●●● ●●● ● ● ● ● ● ● ● ●● ● ●●●● ●●●● ●●● ● ●● ●● ●● ● ● ● ● ● ● ●● ● ●● ● ●●●●● ●●● ●● ●● ● ● ● ● ● ●● ●● ●● ●●● ●●● ●● ●● ● ● ● ● ● Weissella ● ●●●● ● ● ●● ●●● ●● ●●●●● ● ●● ● ● ● ● ● ●● ●●● ● ●● ● ● ●●● ●●● ● ●● ● ● ● ● ● ● ● ●● ●● ● ● ●●●●● ●● ● ●●● ● ● ● ●

● ●● ●●●●● ●●● ● ● ●●●● ●●● ● ● Oenococcus

● ●●●● ●● ●●●●●● ●● ●●● ●● ●● ● ● ● ● ●●●●● ●● ● ●● ●● ●●●●●● ●● ● ● ● ● Fructobacillus ● ●● ● ● ●●●● ●●●● ●●●● ●●● ●● ● ● ●

● ● ● ●●● ● ● ● ●●●● ●● ● ●●●● ●● ●● ● ● ● ● ● ● ●● ● ● ● ●● ● ●●● ●●● ● ● ● ● ● ● ●●● ● ● ●● ●●●● ●●● ● ●● ● ● ● ● ● ●●● ● ● ●● ●● ● ●●●●● ●● ● ● ● ● ●● ●●●● ● ●●●●●● ●●●●● ● ● ● ● ● ● ●● ●●●●●● ● ●●●●●● ●●●●● ●● ● ● ● ● ●● ●●●●● ● ● ●● ●● ●●●●● ● ● ● ● ● Leuconostoc ● ●●●●●● ● ● ●●● ●●●●●●●●● ● ● ● ● ● ● ● ●● ●● ● ●● ● ●●●●● ●●●● ● ●●● ● ● ● ●

●● ● ● ● ●●● ● ● ●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ●● ● ● ● ● ●●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●●● ● ●● ●● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ●●●● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ●●●● ●● ●● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ●● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ●●● ●● ●● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●●● ●●●●● ● ● ●● ● ●●●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ●● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ●● ● ● ● ●●● ● ● ●●●● ● ●● ● ● ● ● ● ● ●● ● ●● ●● ●● ● ●●● ● ● ●● ●● ● ● ●● ● ● ●● ● ● Lentilactobacillus ● ● ●● ● ●●●● ●●●● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ●● ● ● ● ● ● ●● ●● ● ● ●●● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ●●● ● ●● ● ●● ● ● ●●● ●● ● ● ● ● ●● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

● ● ● ●●● ● ● ●● ● ●● ● ●● ● ●● ● ●● ● ● ● ● ● ● ● ●●● ●● ● ● ● ● ● ● ● ● ● ● ●● ●●● ● ● ● ● ● ● ● ● ● ●● ●● ●● ● ●● ● ●●● ● ●● ●● ●● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ●●● ● ●●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ●● ● ● ●● ● ●●● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ●●● ● ●●● ●●● ●● ●●● ● ● ● ● ● ●●● ● ● ●● ●● ●● ● ● ●●● ● ● ●●● ● ●● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ●● ●●● ●●● ●● ● ● ● Secundilactobacillus ● ● ●●● ● ● ● ● ●● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ●● ● ● ● ● ● ●●●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ●●●● ● ● ●●●● ● ● ● ● ● ● ●

● ●● ● ●● ● ●● ● ●● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ●● ● ● ●●● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●●● ● ● ● ● ● ● ●●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ●● ● ● ●● ●● ●●● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ●●● ● ● ● ●● ● ● ● ● ● ● ● ●●● ●● ● ● ● ● ●● ●● ●●●● ● ●●● ●● ● ● ● ● ●● ● ● ● ●● ●● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ●● ● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●●● ● ● ●● ● ● ● ● ● ● ● ● ● ●●●● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● Levilactobacillus ● ● ● ●● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ●●●● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ●● ●●● ● ●● ● ●●● ● ● ● ●● ● ● ●

● ● ● ●● ●●● ● ●●● ● ● ●●● ● ● ● ● ● ● ● ● ●● ●

● ● ● ● ●● ●● ●●● ● ●● ● ●● ● ●● ● ● ●● ● ● ● ● ● ●● ● ●●●● ●●●● ● ● ●● ● ● ● ● ● ● Fructilactobacillus ● ●● ● ● ● ●● ● ●● ●●● ● ● ● ● ●●● ●● ● ●

● ● ●●●● ●● ● ●●● ● ● ● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ●●● ●● ● ●●● ● ● ● ●● ●● ● ●●● ● ●●● ● ● ● ●●●●● ●● ●● ● ● ● ● ●●●● ● ●● ● ● ●●● ● ● ● ●●●●● ● ● ●●● ● ● ● ●●● ●● ● ● ●● ● ● ●● ● ● ● ●● ●●● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● Apilactobacillus ● ● ●● ●●● ● ● ●● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ●● ●● ● ●● ● ● ● ● ●● ● ● ● ● ●● ● ● ● ●

● ● ● ● ●●●●● ● ● ●●●● ● ● ● ● ●● ● ●● ● ● ● ● ●●● ● ●●●●● ●●●● ● ● ● ●● ● ●● ●● ● ● ● ● ● ● ● ● ●●●●●●● ●● ● ●● ●● ●●●●● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ●●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ●● ● ●●●●● ● ●● ● ● ●●● ● ● ●● ● ● ● ● ● ●● ● ●● ●●●● ● ●●●● ●●●● ●● ● ● ●● ● ● ● ● ● ● ●●●● ● ●● ●● ● ●● ● ●● ●●●● ● ● ● ● ● ●● ● ● ●●● ●●● ●●● ●● ●●●● ● ● ● ● ● ● ● ● ●● ●●●●● ●● ● ●● ● ● ● ● ●●●● ●● ● ● ● ● ●● ● ●●●●●● ●● ●●●● ●● ● ● ●● ● ● ● ● ● ● ● ●●● ●●● ● ●●● ●●●● ● ● ●●●● ● ● ● ● ● ● ● ● ●● ● ●● ●● ● ● ● ●● ● ● ●● ●●● ● ● ● ● Limosilactobacillus ● ● ● ●● ●●●●●● ● ● ●● ●● ● ●●● ●● ● ● ● ● ● ● ● ● ●●●● ●●● ● ●● ● ●● ● ●●●● ● ● ● ● ● ●● ● ● ●●● ● ● ●●● ●● ●● ● ● ●● ●●● ●● ● ● ● ● ● ● ●●●●● ● ● ● ● ● ●● ● ● ● ●●● ● ● ● ●

● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●●● ● ● ●● ● ●●● ● ● ● ● ● ● ●● ●● ● ● ● ●● ● ● ●● ●● ●● ● ●●● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ●● ●● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ● ● ● ●●● ●● ● ● ● ● ● Paucilactobacillus ● ● ● ● ●●● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

● ● ● ● ● ● ● ●● ●● ●● ● ● ●●●● ● ● ● ● ● ● ●

● ●● ● ● ● ● ●●●● ● ● ●● ●●●● ●● ● ● ● ● ● ● ● Furfurilactobacillus

● ● ● ● ● ● ● ● ● ●● ●● ●● ●● ● ●● ●● ● ● ● ● ● ● ● ●● ● ●● ● ● ●● ● ●● ●● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ●●● ●● ●● ●● ●● ●● ● ● ● ●● ● ● ●● ● ● ● ● ● ● ● ● ● ●● ●● ● ●● ●●● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ●● ● ●●● ● ●●● ● ●● ●● ● ● ● ● ●● ● ● ● ● ● Lactiplantibacillus ● ● ● ● ● ● ●● ●● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ●●● ● ● ●

● ● ●● ● ● ● ● ●● ● ● ●● ● ● ●●●●● ●● ● ● ● ● ● ● ●● ●● ●● ●● ● ● ●● ● ●●●● ● ●● ● ●● ● ● ● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ●●● ●● ●● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ● ● ● ● ●● ● ● ●● ● ●● ● ● ● ● ● ● ● ● ●● ● ● ●● ● ● ●●● ● ● ●●●● ● ●● ● ● ● ● ● ● ●● ● ● ●● ● ● ●● ● ● ●●● ● ● ● ● ● ●● ● ● ● ● ●● ● ●● ●● ● ●● ●● ●● ● ●● ● ●●●● ● ● ● ● ● ● ●● ● ● ● ● ● ●● ● ●● ●● ● ● ●● ● ● ● ● ●● ● ● Pediococcus ● ● ● ● ● ● ●● ● ●● ● ●●● ● ●●●● ●● ●●● ● ● ● ● ● ●●● ● ● ● ●● ● ●● ● ● ●● ● ●● ● ●●● ●

● ● ●● ● ●● ●●● ● ● ●● ● ●● ● ●●● ●● ● ● ● ● ● ● ● ●● ●● ● ● ● ● ●●● ● ●●●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ●●● ●● ● ● ●● ●●●●● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ●● ●● ●● ●●●● ● ● ● ● ● ● ● ● ● ● ●● ● ●●●● ● ● ● ● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ●● ●● ●●●●●●●● ● ● ● ● ● ● ● ●●● ●● ● ● ● ●●●● ●● ● ●●●●●● ● ● ● ● ● ● ● ● ●● ● ● ● ● ●● ●● ●●● ●●● ● ● ● ● ● ● ● ● ● ●● ●● ●● ● ● ● ● ●● ● ● ●● ●●●●● ● ● ● ● ● ● ● ● ●● ●● ●● ● ● ●●●● ● ●●●● ●●● ● ● ● ● Ligilactobacillus ● ● ● ●● ● ● ●● ● ● ● ●● ●●● ●●●● ● ● ● ● ● ● ● ● ●● ●● ●● ●● ● ● ●● ●●● ●● ●● ●●● ● ● ● ● ● ● ● ● ● ● ●●● ●● ● ● ●● ● ●●● ●● ● ● ●● ● ● ●

● ● ●●● ● ● ●● ●● ●● ●● ● ● ● ●●●● ● ● ● ● ● ● ●● ● ●● ●● ● ●●● ● ● ● ● ●● ● ● ●● ● ● ● ● ● ●●●●● ● ● ●● ● ●●● ●● ● ● ●● ●●● ●● ● ● ● genome ● ● ●● ● ● ●● ● ●● ●●● ● ●● ● ● ●●● ●● ● ● ● ● ● ●● ● ● ● ●●● ● ●●● ● ●● ●● ●● ●●● ● ● ● ● ● ●● ●● ●● ● ●● ● ●●●● ● ● ● ●● ●● ● ● ● ● ● ● ●● ● ● ●● ● ● ● ● ●●●● ●●● ● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ●● ● ●●●●● ● ● ●●● ● ● ● ● ● ● ● ● ●● ●● ● ● ●●● ● ● ●●● ●●● ●●● ● ● ● ● Liquorilactobacillus ● ● ●● ● ● ●●● ● ● ● ● ●●● ●● ●● ● ●●● ● ● ● ● ● ● ●● ● ●●● ●● ● ●●●● ●●● ● ● ● ●● ● ● ● ● ● ● ● ● ●● ●● ●● ●● ● ●●● ●● ●●●● ● ● ● ● ● ●

● ● ●● ● ● ●●●● ●● ● ● ● ● ● ● ● ●● ●● ●● ● ● Dellaglioa

● ● ● ●● ● ●● ● ●● ● ●● ● ● ● ● ●● ●● ● ● ● ● ● ● ●● ● ● ●●●● ● ● ● ● ●● ●●● ● ● ● ●●● ●● ● ● ● ● ● ● ● ● ● ●●● ● ●● ● ● ● ●●●● ● ● ● ●● ● ● ● ● ● ● ● ● ●●● ● ● ● ●● ● ●● ● ● ● ● ●● ●● ● ● ● Loigolactobacillus ● ● ● ● ● ● ● ● ●●● ●● ●● ● ● ● ●● ● ● ● ● ● ● ●

● ● ● ● ● ●●●● ● ●● ● ●● ●●●●● ● ●● ● ● ● Paralactobacillus

● ● ● ● ● ● ● ● ●● ● ●● ●●● ●●● ●● ● ● ●● ●

● ● ● ● ● ● ● ● ● ● ● ●● ●●● ●● ●● ● ●● ● ● ● ● ● ● ● ●● ●● ●● ● ●● ●●●●● ● ● ● ●●● ● Latilactobacillus ● ● ● ● ● ● ● ●●●● ● ●● ● ●●● ● ● ●● ●● ● ●

● ● ● ● ●●● ● ● ● ●● ● ●●●● ●● ● ●●●● ● ● ● ● ● ● ● ● ●●● ● ●●●● ●●●●● ● ● ● ●●● ● ● ● ● ● ●● ●●● ● ● ●●● ●●● ● ● ●●● ●●● ● ● ● ● ●● ● ● ● ● ●● ● ●●● ●● ●●● ●● ●● ● ●● ● ● ● ● ● ● ● ●● ● ●●●●● ●●●●●● ● ● ●● ● ● ● ● ● ●● ●● ● ● ● ●●● ● ●● ●● ● ● ●● ●● ● ● ● ● ●● ● ● ●● ●●●●● ● ● ●●● ● ● ● ● ● ●● ● ● ● ● ● ● ● ●● ●● ● ●●● ●●● ● ● ● ● ● ● ● ●●● ● ● ● ●● ● ● ● ● ●● ●●● ●●●●● ● ●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ●●● ●●● ● ● ●● ●● ● ● ● ● ● ● ● ● ● ●● ● ●●● ● ●●● ● ● ● ● ● ● ● ● ● ● Lacticaseibacillus ● ● ● ● ● ● ●● ● ●● ●●● ●●●● ●● ● ● ● ● ● ● ● ● ● ● ●●● ●● ● ●●● ●●● ●●● ●● ● ● ●● ● ● ● ● ● ● ● ● ●● ● ●● ●● ●●●● ● ●●● ● ● ●

● ● ● ● ● ● ● ● ● ● ● ●● ● ●● ● ● ● ●● ● ● Agrilactobacillus

● ● ● ● ● ● ● ●●●●●●●●●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●●●●● ●●● ● ● ● ●● ● ● ● ● Schleiferilactobacillus ● ● ●● ● ● ●● ● ●●● ●●●●● ● ● ● ● ●●● ● ●

● ● ● ● ●● ● ●●●●● ●●● ● ● ● ● ●● ● ●

● ● ● ● ● ●● ● ● ●●●● ●●●● ●● ● ● ●●●● ● Lapidilactobacillus

●● ● ● ● ●● ●● ●●●●●●●● ● ●●● ● ● ●● ● ● ●● ● ● ●● ● ● ●●●●●●●● ●●●●●●●●●●●●●●●●●●●● ●●●●● ●● ● ● ● ● ● ●● ● ●●● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ●●● ● ● ● ●●● ● ●●●● ●● ● ●●● ●●● ●●●●●●●●●●●●●●●●●●●● ●● ●●● ● ● ● ●●●● ● ●●● ● ●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ●● ● ● ● ●● ● ● ● ● ● ● ●●● ●●●●● ●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●● ●● ● ● ● ●● ● ● ● ● ● ● ●●● ●●●●●● ●●●●●●●● ●●●●●●● ●●●● ● ● ● ● ● ●● ● ● ●●● ● ●●● ●●●●● ●●●●●●●●●●●●●●●●●●● ●●● ● ●●● ● ● ●●● ● ●● ● ●● ●● ●● ●● ●●●●●●●●●●●●●● ●●●●● ●●●● ● ● ● ● ●● ● ●●● ● ● ●●● ●●●●●●●●●● ●●●●●●●●●●●●●●●● ●● ●●●● ● ● Companilactobacillus ●● ● ● ●●● ●●●●●●●● ●●●●●●●●●●●●●●●●●●●●●● ●●●● ● ●●● ● ● ●●● ● ● ●●●●●● ●● ●●●●●●●●●●●●●● ●●●●●●●● ●●●●● ● ● ● ●● ●● ● ● ●● ● ●●●●●●●● ●●●●●●●●●●●●●●●●●●●●● ●●●● ●●● ● ● ●

● ● ● ● ●● ●●●● ●●●●● ● ● ● ● ● ● ● ● ●● ● ● ●● ●●●●●●●● ●●● ● ● ● ● ● Bombilactobacillus ● ● ● ● ● ● ●●●●●●●●●●● ● ●●●● ● ● ●

● ● ● ● ●●●●●●● ●● ●●●●●●● ● ● ● ● ● ● ● ● ● ● ●●●● ● ● ●●● ●●●●●●●●●●●●● ●●●●●● ● ●●●● ● ● ● ● ● ●● ● ● ● ●●● ● ● ●● ● ●●●●●●●● ●●●●●●●●●●●●●●●●●● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●●● ●●●●●●●●●●●●●●●●●● ●●●●●●● ●● ● ● ● ● ● ● ● ●● ● ● ● ●● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●● ●● ● ● ● ● ●● ● ●●● ●● ●● ●●●●●●●●●●●●● ●●●●●●●●●●● ●●● ● ● ●● ● ● ● ● ●● ● ● ● ● ●●● ● ●● ●●●●●●●● ●●●●●●●●●●●●●●●●● ●●●●●● ● ● ● ● ●● ● ● ● ● ●● ●● ● ● ● ● ●●●●●●●●●●● ●●●●●●●●●●●●●●● ●●● ● ●● ● ● ● ● ● ● ● ● ●● ●● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ●● ● ● ●● ● ● ● ● ● ●● ● ●● ● ●●●●●● ●●● ●●●●●● ●●●●●●●●●●● ●● ●●●● ●● ● ●● ● ● ● ●● ● ● ● ●● ●●● ●●●●●●●●●●●●● ●●●●●●●●●●●●● ●●●● ● ● ● ● ● ● ● ● ● ● ●● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ● ● ● ● ● ●● ● ●● ●● ● ● ●●●●●●●●●● ●●●●●●●●●●●●●●●●●●● ● ● ● ● ● ● ● Lactobacillus ● ● ●● ●● ● ● ● ● ●●●●●●●●●● ●● ●●●●●●●●●●● ●●●● ● ● ● ● ● ● ● ● ●●● ●●● ● ●●● ●●●●●●●●●●●●●●●●●●●●●● ●●●● ●● ● ● ● ● ● ● ●● ●● ● ●●● ●● ●●●●●●●●●●●● ●●●●●●●●●●●●●●● ● ● ●● ● ● ● ● ● ● ●● ● ● ● ● ●●●●●●●●●●●●●●●●●●●●●●●●●● ● ● ● ● ● ● ●

● ● ● ● ● ● ● ● ●●● ●● ● ●●●●● ●● ● ● ● Amylolactobacillus

● ● ● ● ● ●● ● ● ●● ● ●● ●●●● ●●● ●● ● ● ● Holzapfelia

0.5 0.6 0.7 0.8 0.9 1.0 top AAI to a genus

own genus ● FALSE ● TRUE Figure S7. Top amino acid identity (AAI) values of genomes to genera. For each genome in genome dataset 2, we selected the highest AAI value with respect to each genus. Dark blue points represent top AAI values of species in the genera that the genomes belong to; light blue points represent top AAI values to species that are classified different genera. When a top AAI value of a genome to a genus is higher than 68%, the genome always belongs to that genus for the genomes in our dataset. Genomes are grouped per genus.

Figure S8. High resolution rendition of Figure 8. Heat map depicting the cAAI values of the 38782 pairwise comparisons of all species in the families Leuconostocaceae and Lactobacillaceae for which genome sequence data was available in August 2019. The source file is provided as Table S3.

Top View