A Taxonomic Note on the Genus Lactobacillus

Taxonomic Description template 1 A taxonomic note on the genus Lactobacillus: 2 Description of 23 novel genera, emended description 3 of the genus Lactobacillus Beijerinck 1901, and union 4 of Lactobacillaceae 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 species (March 2020) that are extremely diverse at phenotypic, 44 ecological, and genotypic levels. This study evaluated the taxonomy 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 acid 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, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, 52 Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, 53 Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, 54 Limosilactobacillus, Fructilactobacillus, 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 microorganisms. The genus is classified in the phylum 68 Firmicutes, class Bacilli, order Lactobacillales, family Lactobacillaceae, which contains the genera 69 Lactobacillus, Paralactobacillus and Pediococcus. The Leuconostocaceae, including the genera 70 Convivina, Fructobacillus, Leuconostoc, Oenococcus and Weissella, 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 peptidoglycan 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” lactic acid bacteria with a simpler differentiation of homofermentative 97 lactic acid bacteria 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 metabolism 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,

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