Supplemental Material:

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

Authors: Baker, J.L.1,*, Morton, J.T.2., Dinis, M.3, Alverez, R.3, Tran, N.C.3, Knight, R.4,5,6,7,

Edlund, A.1,5,*

1 Genomic Medicine Group J. Craig Venter Institute 4120 Capricorn Lane La Jolla, CA 92037

2Systems Biology Group Flatiron Institute 162 5th Avenue New York, NY 10010

3Section of Pediatric Dentistry UCLA School of Dentistry 10833 Le Conte Ave. Los Angeles, CA 90095-1668

4Center for Microbiome Innovation University of California at San Diego La Jolla, CA 92023

5Department of Pediatrics University of California at San Diego La Jolla, CA 92023

6Department of Computer Science and Engineering University of California at San Diego 9500 Gilman Drive La Jolla, CA 92093

7Department of Bioengineering University of California at San Diego 9500 Gilman Drive La Jolla, CA 92093

*Corresponding Authors: JLB: [email protected], AE: [email protected]

ORCIDs: JLB: 0000-0001-5378-322X, AE: 0000-0002-3394-4804

SUPPLEMENTAL METHODS

Study Design. Subjects were included in the study if the subject was 3 years old or older, in good general health according to a medical history and clinical judgment of the clinical investigator, and had at least 12 teeth. Subjects were excluded from the study if they had generalized rampant dental caries, chronic systemic disease, or medical conditions that would influence the ability to participate in the proposed study (i.e., cancer treatment, HIV, rheumatic conditions, history of oral candidiasis). Subjects were also excluded it they had open sores or ulceration in the mouth, radiation therapy to the head and neck region of the body, significantly reduced saliva production or had been treated by anti-inflammatory or antibiotic therapy in the past 6 months. Ethnic origin was mixed for healthy subjects (Hispanic, Asian, Caucasian,

Caucasian/Asian), while children with caries were of Hispanic origin. For the latter group, no other ethnic group enrolled despite several attempts to identify interested families/participants. Children with both primary and mixed dentition stages were included (caries group: 18 children with mixed dentition and 6 with primary dentition; healthy group: 19 children with mixed dentition and 6 with primary dentition). To further enable classification of health status (caries and healthy), a comprehensive oral examination of each subject was performed as described below. Subjects were dichotomized into two groups: caries free (dmft/DMFT = 0) and caries active (subjects with

≥2 active dentin lesions). If the subject qualified for the study, (s)he was to abstain from oral hygiene activity, and eating and drinking for 2 hours prior to saliva collection in the morning. An overview of the subjects and associated metadata is provided in Supplemental Table S1.

Oral examination and study groups. The exam was performed by a single calibrated pediatric dental resident (RA), using a standard dental mirror, illuminated by artificial light. The visual inspection was aided by tactile inspection with a community periodontal index (CPI) probe when necessary. Radiographs (bitewings) were taken to determine the depth of carious lesions. The number of teeth present was recorded and their dental caries status was recorded using decayed (d), missing due to decay (m), or filled (f) teeth in primary and permanent dentitions (dmft/DMFT), according to the criteria proposed by the World Health Organization (1997) (Organization 1971).

Duplicate examinations were performed on 5 randomly selected subjects to assess intra- examiner reliability. Subjects were dichotomized into two groups: caries free (CF; dmft/DMFT=0) and caries active (CA; subjects with ≥2 active dentin lesions). The gingival health condition of each subject was assessed using the Gingival Index (GI) (Loe 1967). GI data was published previously (Aleti et al. 2019). Additionally, parent/guardian of each participant completed a survey regarding oral health regimen.

Radiographic assessment. Bitewing radiographs were analyzed on the XDR Imaging Software

(Los Angeles, CA). Lesion depth was determined with the measuring tool, and categorized as follows: E1 (radiolucency extends to outer half of enamel), E2 (radiolucency may extend to the dentinoenamel junction), D1 (radiolucency extends to the outer one-third of dentin), D2

(radiolucency extends into the middle one third of dentin), and D3 (radiolucency extends into the inner one third of dentin)(Anusavice 2005). To calculate the depth of lesion score, the following scores were assigned to each lesion depth: E1 = 1, E2 = 2, D1 = 3, D2 = 4, and D3 = 5, afterwards a total depth score was calculated for each subject.

Saliva collection. Unstimulated saliva was collected between 8:00-11:00am for the salivary immunological marker analysis. Subjects were asked to abstain from oral hygiene activity, and eating and drinking for two hours prior to collection. Before collection, subjects were instructed to rinse with water to remove all saliva from the mouth. In this study, unstimulated saliva was collected for salivary immunological marker analysis, while stimulated saliva (by chewing on sterile parafilm) was collected for Illumina sequencing (to dilute and amount of human DNA and material present). 2 ml of unstimulated saliva was collected from subjects by drooling/spitting directly into a 50mL Falcon conical tube (Fisher Scientific, Pittsburg PA) at regular intervals for a period of 5-20 minutes. Saliva samples were immediately placed on ice and protease inhibitor cocktail (Sigma, MO, USA) was added at a ratio of 100uL per 1mL of saliva to avoid protein degradation. Then saliva samples were processed by centrifugation at 6,000 x g for 5 min at 4°C, and the supernatants were transferred to cryotubes. The samples were immediately frozen in liquid nitrogen and stored at -80 °C until analysis. 2 ml of stimulated saliva was collected immediately following collection of unstimulated saliva.

Sequencing read quality control. As reported in Aleti et al., 2019, raw Illumina reads were subjected to quality filtering and barcode trimming using KneadData v0.5.4 (available at https://bitbucket.org/biobakery/kneaddata) by employing trimmomatic settings of 4-base wide sliding window, with average quality per base >20 and minimum length 90 bp. Reads mapping to the human genome were also removed. KneadData quality control information is provided in

Supplemental Table S1.

Assembly and binning of MAGs. metaSPAdes was utilized to de novo assemble metagenomes from the quality-filtered Illumina reads (Nurk et al. 2017). A separate assembly was performed for each sample, as opposed to a co-assembly assembly of all samples, an alternative approach used by some studies. The pros and cons of a co-assembly versus individual assemblies have been discussed previously (Pasolli et al. 2019). The resulting assemblies were binned using the

MetaWRAP pipeline v1.1.5 (Uritskiy et al. 2018). The MetaWRAP initial_binning module used

Maxbin2 (Wu et al. 2016), Metabat2 (Kang et al. 2019), and Concoct (Alneberg et al. 2014).

Subsequently, the bin_refinement module was used to construct the best final bin set by comparing and selecting the most complete and least contaminated results of the 3 binning tools.

The bin_reassembly module was then used to reassemble the refined bin set to further improve the final bins. The quality control cutoffs for all MetaWRAP modules were >50% completeness and <10% contamination, which are the cutoffs for Medium-Quality Draft Metagenome-

Assembled Genomes as described by the Genome Standards Consortium (Bowers et al. 2017).

This approach generated 527 metagenome-assembled genomes (MAGs) that were at least of medium quality. Generally speaking, the samples with deeper sequencing provided more bins meeting this threshold, with sample SC33, with 249 million non-human reads yielding 69 bins, while sample SC26, with 1.4 million non-human reads yielding just 3 bins. The metaWRAP classify_bins and quant_bins modules were used to respectively obtain a taxonomy estimate and to provide the quantity of each bin in the form of ‘genome copies per million reads’.

Dereplicating to species-level genome bins. As a result of the individual assemblies, many of the 527 MAGs were likely to represent redundant species across samples. fastANI (Jain et al.

2018) was used to compare the ANI of all 527 MAGs and generate a distance matrix that was used to dereplicate the MAGS into SGBs using a cutoff of 95%ANI. This distance matrix was visualized using Cytoscape (Shannon et al. 2003) (Figure 1A). Although a topic of some debate,

95%ANI has been used by several recent landmark studies as the cutoff for genomes representing the same species (Jain et al. 2018). To taxonomically identify species-level genome bins (SGBs), Mash v2.1 (Ondov et al. 2016) was used to query all 527 MAGs against the entire

RefSeq database with a Mash distance cutoff of 5 (corresponding to a 95% average nucleotide identity (ANI)). All MAGs with a RefSeq hit with a Mash distance of <5 were assigned the species name of that hit. The fact that Mash distance <5 and fastANI ANI>95% aligned almost perfectly served as a useful internal control. There were several rare occasions in this dataset where

SGBs, as defined by the 95% ANI distance matrix, included MAGs that best matched different

(although closely related) RefSeq references. Whether this indicates that 95% ANI is not stringent enough (e.g. these should in fact be classified as multiple species) or too stringent (e.g. they should all be classified as the same species) is a debate beyond the scope of this work. This approach yielded 90 known species-level-genome bins (kSGBs), representing 399 MAGs with ³95% ANI to a RefSeq genome (based on Mash), and 60 unknown SGBs (uSGBs), representing

128 MAGs (Figure 1A-G), with no genome in RefSeq with an ANI ³95% (Figure 1A-G). MAG pie charts (Figure 4B-C) were created using Microsoft Excel and MAG quality violin chart were created using Graph Pad Prism. Statistical significance was determined using a Tukey’s multiple comparisons post-test following a one-way ANOVA using Graph Pad Prism.

Determining taxonomy of unknown SGBs (uSGBs). Here, a strategy for classifying uSGBs into genus-level genome bins (GGBs), which have a 85%-95% ANI to a GenBank genome, and family-level genome bins (FGBs), which have no match ³85% ANI to a GenBank genome, was employed, similar to the method described in Pasolli et al., 2019. The predicted family for each

MAG was first inferred using the CheckM (Parks et al. 2015), Kraken (Wood and Salzberg 2014), and classify_bins tools from within the MetaWRAP pipeline. Next, because there are publicly available, and in many cases described, genomes in GenBank that do not appear in the RefSeq database used by Mash, each uSGB was compared against all GenBank genomes in its predicted family using fastANI. This process reassigned 18 uSGBs (rSGBs), representing 31 MAGs, to kSGBs, as they had ³95% ANI match in GenBank (Supplemental Table S2). For the remaining

“true” uSGBs, 20 uSGBs, representing 48 MAGs, that had 85%-95% ANI match to a GenBank genome were termed genus-level genome bins (GGBs), as the genus can be assigned with a fair amount of confidence, while the species appears to be not previously described. The final 22 bins, representing 49 MAGs, had no matching reference in GenBank with an ANI ³85%. These were termed family-level genome bins (FGBs), as the family or higher-level taxa can be inferred, but the MAGs likely represent novel genera. When uSGBs contained multiple MAGs, the MAG with the best quality score according to the formula (completion – (2x contamination)) was used to find the best hit.

Phylogenetic placement of uSGBs. Anvi’o (Eren et al. 2015) was used to determine the phylogeny of the Saccharibacteria kSGBs and uSGBs. The Anvi’o Snakemake (Koster and

Rahmann 2012) phylogenomics workflow utilizes muscle (Edgar 2004), trimAl (Capella-Gutierrez et al. 2009), and IQ-TREE (Nguyen et al. 2015). PhyloPhlAn2 (Pasolli et al. 2019) was used to determine the phylogeny of Clostridiales and Bacteroidales uSGBs. The following parameters were used: --diversity medium –accurate. The following PhyloPhlAn2 external tools were used: diamond (Buchfink et al. 2015), mafft (Katoh and Standley 2013), trimAl (Capella-Gutierrez et al.

2009), fasttree (Price et al. 2009), and RAxML (Stamatakis 2014). Resulting phylogenetic trees were visualized using iToL 4(Letunic and Bork 2019). Anvi’o was utilized to examine

Saccharibacteria phylogeny because its pipeline was more amenable to the highly reduced number of single copy marker genes found in Saccharibacteria genomes. PhyloPhlAn2 was used to examine Bacteroidales and Clostridiales phylogeny because, compared to Anvi’o, it requires less preprocessing of the reference and sample genomes prior to actual phylogenetic analysis, making the pipeline more appropriate for these queries that have hundreds or thousands of genomes. Labels on the Bacteroidales and Clostridiales trees in Figure 2A-B indicate the genus of the GGB, and the family and most-closely related genus of the FGBs, as determined by fastANI against all Bacteroidales or Clostridiatles in GenBank. The Saccharibacteria clades were based upon the phylogeny and reference genomes published in (Figure 2C)(McLean et al. 2020).

Differences in the phylogeny reported here compared to (McLean et al. 2020) are likely to result from a different set of marker genes used to construct the phylogeny.

Pangeomics and functional enrichment. Individual assembled genomes were annotated with

Anvi’o (COG Functions) and eggnog-mapper v2 (Huerta-Cepas et al. 2017; Huerta-Cepas et al.

2019). Anvi’o was utilized to perform pangenomics analysis (Delmont and Eren 2018). This pipeline also utilized HMMSEARCH (Eddy 2011) and INFERNAL (Nawrocki and Eddy 2013). tRNAs were predicted using Anvi’o and 16S rRNA genes were predicted using the cmsearch function of INFERNAL. 16S rRNA sequences were identified using the HOMD 16S rRNA

Sequence Identification page of the expanded Human Oral Microbiome Database (eHOMD, http://www.homd.org/, (Escapa et al. 2018). To examine strain-level differences between caries and health-associated isolates, SGBs with at least 4 representatives from healthy subjects and 4 representatives from caries subjects were considered. 13 SGBs met these criteria: Atopobium sp. ICM42b, Eubacterium sulci, Haemophilus parainfluenzae, Candidatus Lachnospiraceae

FGB2, Mogibacterium diversum, Megasphaera micronuciformis, Prevotella histicola, Prevotella

ICM33, Porphymonadaceae bacterium KA00676, Prevotella pallens, Prevotella salivae,

Peptostreptococcus GGB1, and Candidatus Solobacterium GGB1. Pangenomes of these SGBs and significantly enriched functional pathways between caries and health-associated isolates were examined using Anvi’o. There were no significantly enriched gene clusters in caries compared to health, or vice versa, within these pangenomes. Meanwhile, a pangenome of the

Saccharibacteria genomes and several reference strains was examined, and there was a large amount of functional pathway enrichment between Saccharibacteria clades (Figure 3B-C,

Supplemental Fig.S3A-B). KEGG KO Functional pathway occurrence frequency across the

Saccharibacteria clades was exported using Anvi’o, and used to create the metabolic network in

Supplemental Fig. S5B using KEGG Mapper (https://www.genome.jp/kegg/mapper.html).

Inference of actively replicating taxa. iRep was utilized (Brown et al. 2016) to estimate which taxa identified in the metagenomics analysis were alive and metabolically active, and to compare this data between health- and caries-associated microbiomes. iRep infers replication rates based upon differential sequencing coverage of genomic regions with respect to the origin of replication

(Brown et al. 2016). iRep requires 75% completeness, <175 contigs per 1mb, and looks at contigs

> 5000bp with a > 5 average coverage. iRep was able to compute replication rates for 183 of 527

MAGs. The replication rate of all bacteria was not significantly different among the taxa derived from the saliva of healthy children compared to the saliva from the children with caries (Supplemental_Fig_S6.pdf). At the individual SGB level, there were only 8 SGBs with sufficient

(at least 3) MAGs, which passed the requirements for iRep, from both the healthy and the caries groups. None of these 8 SGBs had statistically different rates of replication between the healthy and caries groups (Supplemental_Fig_S6.pdf).

Genome-based taxonomic abundance analysis. Overall, the taxonomy of the assembled

MAGs largely reflected the taxonomy of the communities predicted by MetaPhAn2. One notable exception was the lack of Streptococci among the assembled bins. Difficulty assembling quality

Streptococcal genomes from metagenomics datasets has been noted previously (Espinoza et al.

2018), and is thought to occur because the high promiscuity of Streptococcus k-mers (due to high intra-genera diversity within Streptococcus, particularly from oral samples). Assembly biases such as this are examples that support use of unassembled reads for taxonomic abundance profiling and similar analyses, as performed by MetaPhlAn2 and the downstream tools in this study. However, the taxa in the MetaPhlAn2 database do not match exactly with the taxa of the genomes assembled from these microbiomes, and it was difficult to determine whether any of the novel taxa assembled here are detected by MetaPhlAn2. To examine the abundances of the taxa with assembled genomes in this study, a BWA index was created using a database consisting of the best quality (completion – (2 x contamination)) genome from each SGB in this study. The post-QC sequencing reads were mapped to the database using BWA-MEM (Li et al. 2009; Li

2014). This was used to create taxonomic abundance table, which was analyzed by DEICODE

(Supplemental Fig. S6C). Many of the overall trends were preserved compared to the DEICODE analysis of the unassembled reads, and several novel taxa (Candidatus Nanosynbacter GGB3 and GGB4, and Candidatus Gracilibacteria FGB1) appeared to be associated with caries

(Supplemental Fig. S6C). However, the authors recommend utilizing unassembled reads for abundances purposes to avoid biases introduced by the assembly process. A significant difference in beta divsersity between the healthy and caries groups was observed by

PERMANOVA performed using the QIIME2 diversity plugin.

Read-based taxonomy. Filtered reads were then analyzed using MetaPhlAn2 v2.7.5 (Truong et al. 2015) to determine relative abundances of taxa. The predicted total number of reads for each sample was multiplied by the relative abundances of each taxa within the sample to obtain an estimated number of reads of each taxa. The resulting OTU table was utilized for downstream diversity and correlation analysis. Unlike 16S sequencing, metagenomic sequencing detects viruses and eukaryotes in addition to bacteria. 12 viruses were detected in this study, including several human herpesviruses and several bacteriophage (Supplemental Fig. S4A,B,D). The viruses were detected at relatively low frequency and did not appear to be significant drivers of beta diversity in this study group (Figure 4A). The fungal pathogen, Candida albicans is known to be involved in pathogenesis in many cases of dental caries (reviewed in (Pereira et al. 2018)), therefore it was surprising that it was not detected by MetaPhlAn2 in this study. Mapping Illumina reads directly to the C. albicans genome indicated the presence of C. albicans in the samples, but the number of reads was small, and thus any fungal pathogens present in the study group were likely to be below the threshold of detection employed in taxonomic quantification by

MetaPhlAn2 (data not shown). This is likely in part due to the use of DNA extraction methods designed for bacteria, not fungi.

Diversity analyses. The taxonomic abundance table (i.e. OTU table) generated from

MetaPhlAn2 was used as input for QIIME2 (Bolyen et al. 2019). The QIIME2 diversity plugin was used to calculate alpha diversity (within sample diversity) (Bolyen et al. 2019). The QIIME2 plugin,

DEICODE (Martino et al. 2019), was used to calculate beta diversity with feature loadings.

DEICODE utilizes matrix completion and robust Aitchison principal components analysis (PCA), providing several advantages over other tools, including the ability to accurately handle sparse datasets (e.g. in most microbial communities, most taxa are not present in a majority of samples), scale invariance (negating the need for rarefaction) and preservation of feature loadings (i.e. which taxa are driving the differences in PCA ordination space)(Martino et al. 2019). The resulting ordination was visualized using the QIIME2 plugin Emperor (Vazquez-Baeza et al. 2013). Taxa ranks driving differences in ordination space along axis 2 (the axis with the most difference in disease status) were visualized using Qurro . A significant difference in beta diversity between the caries and healthy groups was observed with a PERMANOVA using the QIIME2 diversity plugin.

Taxa associated with disease. The OTU table generated by MetaPhlAn2 was used as input for

Songbird (Morton et al. 2019b), to rank species association with disease status. Songbird utilizes reference frames to rank the association of taxa with a given metadata category, and alleviates many of the issues caused by the compositional nature of sequencing data. Because this method is sensitive to sparsity, only species observed in at least 10 samples and having over 10,000 total predicted counts were analyzed. The following parameters were used in the songbird multinomial script: number of random test examples: 5, epochs: 50,000, batch size: 8, differential-prior: 1, learning rate: 0.001. Taxa ranks were visualized using Qurro. Log ratios of Prevotella to Rothia,

Haemophilus, or Neisseria were extrapolated using Qurro, and graphed using Graph Pad Prism.

Significance was determined using a Welch’s t-test between groups, performed by Graph Pad

Prism.

Functional profiling and diversity. HUMAnN2 (Franzosa et al. 2018) was used to provide abundance information about the functional pathways present in the metagenomes, which was also stratified by species. QIIME2, DEICODE, Songbird, Emperor, and Qurro were utilized to analyze the unstratified functional pathway data in a manner similar to that described for the taxonomic abundance information as described above. Significant differences in alpha and beta diversity between the healthy and caries groups was observed with a Kruskal-Wallis test and a

PERMANOVA, respectively, using the QIIME2 diversity plugin. Contributional diversity, as plotted in Figure 5C, was examined across the 69 core pathways that were present in each sample, and had at least 3 taxa contributing to the pathway. Contributional alpha and beta diversity of these pathways were calculated using QIIME2.

Species-immunological marker co-occurrences. The co-occurrences of species and immunological markers was estimated using neural networks via mmvec (Morton et al. 2019a). mmvec uses neural networks for estimating microbe-metabolite interactions through their co- occurrence probabilities. The following parameters were used: number of testing examples: 5, minimum feature count: 10, epochs: 1000, batch size: 3, latent dim: 3, input prior: 1, output prior:

1, learning rate 0.001. The QIIME2 Emperor plugin was used to visualize the resulting ordination.

SUPPLEMENTAL FIGURES

Figure S1 Summary of study design A

Healthy group Collection of Centrifugation to Illumina 2 ml unstimulated DNA extraction 24 children (age 6-11 years) remove large debris sequencing healthy dentition saliva

Caries group Collection of Centrifugation to multiplex Luminex 2 ml stimulated 23 children (age 6-11 years) remove large debris immunoassay saliva > 2 active dentin caries

B

Input data Bioinformatics/Metagenomics Pipeline Intermediate data

Final data Reconstructed metagenome- Quality control Ensemble binning Bin Refinement assembled genomes (MAGs) & (MetaWRAP) Measure Illumina reads Removal of Maxbin2 bins Bin 287 Medium-Quality human reads Assembly Reassembly (completeness >50% replication rate Replication High-quality 24 healthy Concoct bins Final Bins contamination <10%) rate of MAGs reads iRep 23 caries KneadData metaSPAdes MetaWRAP Metabat2 bins 240 High-Quality MetaWRAP (completeness >90% contamination < 5%) fastANI: Funactional Dereplicate to SGBs >95% ANI Taxonomic MetaPhlAn2 pathway HUMAnN2 distance matrix abundances abundances 151 total species-level genome bins (SGBs) Mash: Taxonomic abundance Pathway abundance Assign Taxonomy < 5 Mash distance table table RefSeq to RefSeq genome Beta diversity Beta diversity Mash database with with Multinomial Multinomial 95 known SGBs feature loadings DEICODE Songbird feature loadings DEICODE Songbird regression regression (376 MAGs) Aitchison Taxa ranks Aitchison Taxa ranks 56 unknown SGBs PCA plot associated with PCA plot associated with (126 MAGs) disease status disease status Manual taxonomic fastANI against GenBank Visualize Visualize Visualize Visualize Qurro Qurro Qurro Qurro annotation of uSGBs MetaWRAP taxa ranks taxa ranks taxa ranks pathway ranks GenBank Kraken database BlastX Unsupervised Supervised Unsupervised Supervised Final bins with taxonomy taxa rankings taxa rankings pathway rankings pathway rankings Co-occurance (colored by appearance in analysis network below) Phylogenetic mmvec analysis of 90 SGBs (399 MAGs) Phylogenetic uSGBs Microbe-marker Immunological trees of uSGBs co-occurances PhyloPhlAn2 18 uSGBs re-assigned marker concentrations Anvi’o to kSGBs 24 healthy Pathway-marker 20 GGBs (genus-level GB) 23 caries co-occurances (48 MAGs) Pangenome (known genus, novel species) Functional analysis enrichment 22 FGBs (family-level GB) Anvi’o (49 MAGs) (known family, novel genus) Supplemental Fig. S1: Overview of study design and bioinformatics methods. (A) Flow chart illustrating the steps taken to get from clinical specimen to bioinformatics data. (B) Flow chart illustrating the computational methodology utilized in this study. Input data is in yellow boxes, intermediate data is in blue boxes, and final data is in green boxes. For each step, the tool(s) or package(s) used are provided in italics. The ‘Final bins with taxonomy’ box is color- coded to match the metagenome-assembled genome (MAG) average nucleotide (ANI) network in Fig. 1.

Figure S2 Candidatus_Azobacteroides_pseudotrichonymphae_genomovar._CFP2

Proteiniphilum_saccharofermentans_isolate_M3/6_genome

Porphyromonadaceae_bacterium_NLAE-zl-C104

Dysgonamonadaceae_bacterium_strain_XHS2771

Petrimonas_mucosa_isolate_ING2-E5A_genome

Porphyromonadaceae_bacterium_KH3CP3RA

Dysgonomonas_macrotermitis_strain_DSM_27370 Porphyromonadaceae_bacterium_ING2-E5B Porphyromonadaceae_bacterium_KH3R12 Bacteroidetes_bacterium_strain_bin_5_strain_JCVI_32_bin.69

Porphyromonadaceae_bacterium_KHP3R9

Dysgonomonas_gadei_ATCC_BAA-286 Porphyromonadaceae_bacterium_COT-184_OH4590 Coprobacter_secundus_strain_177 Candidatus_Symbiothrix_dinenymphae_DNA Butyricimonas_synergistica_isolate_43_13_Ley3_66761_scaffold_1044 Paludibacter_sp._SCN_50-10_ABS72_C0001 Dysgonomonas_mossii_DSM_22836

A Tannerella_sp._CAG:118 Bacteroidales_bacterium_45-6

Paludibacter_propionicigenes_WB4 Dysgonomonas_sp._37-18

Odoribacter_splanchnicus_strain_NCTC10825

Paludibacter_sp._47-17

Paludibacter_jiangxiensis_ Odoribacter_splanchnicus_strain_An39 Odoribacter_laneus_YIT_12061Odoribacter_laneus_CAG:561 Odoribacter_splanchnicus_CAG:14 Alistipes_sp._58_9_plus_Ley3_66761_scaffold_10234

Sanguibacteroides_justesenii_strain_OUH

Sanguibacteroides_justesenii_strain_OUH Odoribacter_sp._CAG:788

Bacteroides_sp._CAG:144

Tannerella_sp._CAG:51 Coprobacter_fastidiosus_NSB1

Tannerella_sp._6_1_58FAA_CT1 Barnesiella_intestinihominis_YIT_11860

Bacteroides_sp._CAG:20

Barnesiella_sp._An22

Barnesiella_sp._An55

Barnesiella_viscericola_DSM_18177

Prevotella_sp._CAG:279 Prevotella_sp._CAG:485

Bacteroides_sp._CAG:927 Muribaculum_intestinale_strain_YL27

Prevotella_sp._CAG:1031 Butyricimonas_sp._An62 Prevotella_sp._CAG:873 Macellibacteroides_sp._HH-ZS Parabacteroides_chartae_strain_DSM_24967 Alistipes_sp._56_sp_Nov_56_25_Ley3_66761_scaffold_102Alistipes_finegoldii_strain_2789STDY5834947 Bacteroidales_bacterium_Barb7 Bacteroidales_bacterium_Barb4 Bacteroidales_bacterium_Barb6XT Alistipes_finegoldii_DSM_17242 Bacteroidales_bacterium_Barb6 Parabacteroides_sp._An277

Parabacteroides_sp._merdae-related_45_40_Ley3_66761_scaffold_1018

Alistipes_onderdonkii_strain_An90 Parabacteroides_merdae_CAG:48

Parabacteroides_merdae_CL09T00C40 Alistipes_sp._HGB5 Alistipes_finegoldii_CAG:68 Parabacteroides_johnsonii_CAG:246 Alistipes_timonensis_JC136_strain_DSM_25383_ Parabacteroides_merdae_strain_2789STDY5834848

Parabacteroides_johnsonii_strain_An42

Parabacteroides_johnsonii_CL02T12C29 Parabacteroides_goldsteinii_dnLKV18

Parabacteroides_sp._ASF519 Alistipes_shahii_WAL_8301 Parabacteroides_chinchillae_strain_DSM_29073 Alistipes_sp._CAG:29 Parabacteroides_goldsteinii_CL02T12C30

Parabacteroides_gordonii_MS-1

Alistipes_sp._CAG:53 Parabacteroides_sp._HGS0025 Parabacteroides_sp._CAG:409

Parabacteroides_distasonis_str._3776

Bacteroides_sp._2_1_33B

Parabacteroides_sp._AT13 Alistipes_sp._CHKCI003_isolate_CHKC3 Alistipes_sp._An31A Parabacteroides_sp._CT06

Alistipes_sp._An54 Parabacteroides_distasonis_str._3776 Alistipes_sp._An116 Parabacteroides_sp._CAG:2

Parabacteroides_sp._20_3 Alistipes_sp._CAG:268Alistipes_sp._An66 Parabacteroides_sp._D13 Alistipes_putredinis_DSM_17216Alistipes_putredinis_CAG:67 Parabacteroides_sp._D26

Parabacteroides_sp._D25

Mucinivorans_hirudinis_complete_genome Porphyromonas_sp._31_2_genomic Alistipes_indistinctus_YIT_12060Alistipes_sp._CAG:157 Bacteroides_sp._3_1_19 Alistipes_inops_strain_627 ain_COT-109 Parabacteroides_sp._2_1_7 _str Tannerella_forsythia_strain_WW10960

Tannerella_forsythia_strain_9610

Bacteroides_sp._CAG:709 Tannerella_sp._oral_taxon_808 C065F10 Tannerella_sp._oral_taxon_BU063s_cangingivalis Bacteroides_sp._CAG:770 F02 Tannerella_sp._oral_taxon_BU063 Bacteroides_sp._CAG:545 p._HMS 077 Tannerella_sp._oral_taxon_808 SC romonas_cangingivalis_strain_COT-109 Porphyromona Bacteroidales_bacterium_WCE2008Alistipes_sp._CAG:435 rphy romonas_s Po Bacteroidales_bacterium_WCE2004Alistipes_sp._CAG:514 Porphy

Porphyromonas_sp._CAG:1061

Bacteroides_sp._CAG:1060 Porphyromonas_sp._HM Candidatus_Bacteroides_periocalifornicus_isolate_12B Bacteroidales_bacterium_CF Porphyromonas_sp._COT-108_OH2963

Porphyromonas_canoris_strain_COT-108

Alistipes_sp._CAG:831 Porphyromonas_sp._COT-108_OH1349 Bacteroides_sp._SM23_62_WORSMTZ_10170 Porphyromonas_canoris_strain_COT-108 bacterium_A7P-90m_ Bacteroidales_bacterium_TBC1 Porphyromonas_crevioricanis_strain_COT-253 Porphyromonas_crevioricanis_strain_COT-253 Elizabethkingia_meningoseptica_strain_KC1913 Bacteroides_pectinophilus_CAG:437 Porphyromonas_uenonis_60-3_deg1118640599757

Elizabethkingia_meningoseptica_strain_EM1 Porphyromonas_asaccharolytica_PR426713P-I_bacterium_KA00251 dales Porphyromonas_asaccharolytica_DSM_20707umdentaria_strain_ATCC_51356 Bacteroi _circ _strain_COT-192 Porphyromonas_endodontalis_ATCC_35406 phyromonas Por

Porphyromonas_gingivicanis_strain_COT-022 hyromonas_macacaes_macacae_strain_COT-192 ona Porp

Porphyrom

Porphyromonas_gingivalis_strain_WW2952 yromonas_gulae_strain_COT-052 Porph ngivalis_TDC60 s_gi Porphyromonas_sp._COT-052_OH4946

Porphyromona

Porphyromonas_gulae_strain_COT-052

Porphyromonas_sp._COT-239_OH1446

Porphyromonas_sp._COT-290_OH3588 Candidatus_P Porphyromonas_sp._COT-290_OH860 Candidatus_Prevotellaceae_FGB3_strain_JCVI_19_bin.13re votellaceae_FGB3 Candidatus_Porphyromonadaceae_FGB2_JCVI_44_bin.40

Candidatus_Prevotellaceae_FGB3_strain_JCVI_47_bin.22 Porphyromonas_sp._oral_taxon_279 _strain_JCVI_30_bin.3 phyromonas_catoniae_ATCC_51270catoniae_F0037 Candidatus_Prevotellaceae_FGB3_strain_JCVI_23_bin.18 Por Porphyromonas_ Candidatus_Prevotellaceae_FGB3_strain_JCVI_32_bin.40 Porphyromonas_somerae_strain_KA00683

Porphyromonadaceae_bacterium_KA00676nas_sp._oral_taxon_278 Prevotella_multi o nadaceae_FGB1_JCVI_44_bin.22 Porphyrom romo saccharivorax_DSM_17128 Prevotella_sp._S7-1-8_contig001 Candidatus_Porphy C Prevot Porphyromonas_sp._KLE_1280 ella_bergensis_DSM_17361 s_coprosuis_DSM_18011 Bacteroide Bacteroidales_bacterium_KA00344 Bacteroides_sp._CAG:462 Prevotella_dentali a_sp._An20 rrane Medite s_DSM_3 alanitronis_DSM_18170 Prevotella_dentalis_ 688 Bacteroides_s DSM_ Prevotella_sp._HMSC077E093688 ides_sp._An269 Bactero An279 Prevotell a_macu Bacteroides_sp._ losa_OT_289 Prevotella_oris_C735 Bacteroides_sp._An19 ._An51A Prevotella_sp._HMSC069G02 Bacteroides_sp Genomes identified in this study cteroides_sp._CAG:702 Prevotella_oris_F0302 Ba Prevotella_sp._HMSC077E08 Bacteroides_sp._An322 Bacteroides_sp._CAG:714 Prevotella_salivae_F0493 Bacteroides_coprocola_DSM_17136 Prevotella_oulorum_F0390 Bacteroides_plebeius_DSM_17135 Prevotella_oulorum_strain_ATCC_43324 Bacteroides_plebeius_CAG:211 Prevotella_salivae_DSM_15606 Bacteroides_sp._CAG:875 Prevotella_sp._S7_MS Bacteroides_coprophilus_DSM_18228 Prevot ella_sp._DNF00663 Bacteroides_coprophilus_CAG:333

Prevotella_baroniae_F0067 Bacteroides_coprocola_CAG:162

Prevotella_copri_CAG:164 Bacteroides_sp._CAG:530

Prevotella_copri_strain_2789STDY5834881 Bacteroides_sp._CAG:1076

Prevotella_copri_strain_Indica Bacteroides_sp._CAG:443

Prevotella_sp._CAG:1092 Bacteroides_sartorii_ Candidatus_Gracilibacteria_FGB1_strain_JCVI_11_bin_10 Prevotella_sp._CAG:386 Bacteroidales Bacteroides_dorei_CAG:222 Bacteroides_massiliensis_B84634 Candidatus_Absconditabacteria_sp_SR1_MAG_IV_A_1_strain_JCVI_32_bin.67 Prevotella_sp._CAG:732 candidate_division_TM7_single_cell_isolate_TM7b_contigs Bacteroides_dorei_CL03T12C01 Prevotella_sp._CAG:604 Candidatus_Saccharibacteria_W2P28042_contigs Bacteroides_vulgatus_str._3775 Prevotella_bryantii_strain_KHPX14 Candidatus_Saccharibacteria_Baikal_deep_G207_contigs Bacteroides_sp._CAG:98 Prevotella_bryantii_B14 Candidatus_Saccharibacteria_SW_7_54_9SW_7_54_9_contigs Bacteroides_vulgatus_dnLKV7 Candidatus_Saccharibacteria_QS_8_54_8QS_8_54_8_contigs Prevotella_buccae_D17 Bacteroides_sp._9_1_42FAA Candidatus_Saccharibacteria_QS_5_54_17QS_5_54_17_contigs CPR outgroup Prevotella_sp._MSX73 Bacteroides_vulgatus_CAG:6 Candidatus_Saccharibacteria_CSSed165cm_563_contigs

Bacteroides_sp._3_1_33FAA Candidatus_Saccharibacteria_SZUA_65_contigs Prevotella_buccae_ATCC_33574 Candidatus_Saccharibacteria_SB0662_bin_47_contigs Prevotella_pleuritidis_F0068 Bacteroides_dorei_CL02T00C15 Candidatus_Saccharibacteria_CSBr16_101_contigs Bacteroides_sp._4_3_47FAA Prevotella_enoeca_strain_F0113 Leaves Candidatus_Saccharibacteria_CSSed165cm_431_contigs Prevotella_sp._CAG:487 Bacteroides_sp._3_1_40A Candidatus_Saccharibacteria_CSSed11_228_contigs Prevotella_sp._CAG:1320 Tree scale: 0.1 Bacteroides_sp._CAG:661 Candidatus_Saccharibacteria_CSSed11_200R1_contigs Prevotella_sp._P3-122 Bacteroides_sp._CAG:598 Candidatus_Saccharibacteria_RIFCSPHIGHO2_12_FULL_41_12_contigs Bacteroides_sp._CAG:633 Candidatus_Saccharibacteria_DOLJORAL78_51_182_contigs Prevotella_sp._CAG:924 Candidatus_Saccharibacteria_SZUA_462_contigs GGBs Bacteroides_oleiciplenus_YIT_12058 Candidatus_Saccharibacteria_Bin10_2_contigs Prevotella_sp._ICM33 Bacteroides_intestinalis_DSM_17393 Candidatus_Saccharibacteria_YM_S32_TM7_50_20strain_YM_S32_TM7_50_20_contigs Prevotella_melaninogenica_DNF00666_contig001 Bacteroides_oleiciplenus_isolate_45_34_Ley3_66761_scaffold_104 Candidatus_Saccharibacteria_CG19_WC_8_21_14_NA_150_51_44_contigs Prevotella_melaninogenica_D18 Bacteroides_stercorirosoris_strain_DSM_26884 Candidatus_Saccharibacteria_UBA4723UBA4723_contigs Prevotella_fusca_JCM_17724 Bacteroides_intestinalis_CAG:564 Candidatus_Saccharibacteria_UBA4665UBA4665_contigs FGBs Bacteroides_intestinalis_CAG:315 Candidatus_Saccharibacteria_palsa_1325_contigs Bacteroides_intestinalis_strain_KLE1704 Candidatus_Saccharibacteria_palsa_1333_contigs Prevotella_scopos_JCM_17725_strain_W2052_ Bacteroides_cellulosilyticus_DSM_14838 Candidatus_Saccharibacteria_UBA5150UBA5150_contigs Prevotella_scopos_JCM_17725_strain_DSM_22613Prevotella_jejuni_strain_DSM_26989 Bacteroides_cellulosilyticus_strain_CL09T06C25 Candidatus_Saccharibacteria_CG_4_10_14_0_2_um_filter_52_9CG_4_10_14_0_2_um_filter_52_9_contigs Prevotella_sp._F0091 Bacteroides_cellulosilyticus_CAG:158 Candidatus_Saccharibacteria_UBA4729UBA4729_contigs Prevotella_jejuni_strain_CD3:33_chromosomePrevotella_sp._C561 SGBs (reassigned only) Candidatus_Saccharibacteria_UBA6224UBA6224_contigs Bacteroides_helcogenes_P_36-108

Bacteroides_sp._AR29 Candidatus_Saccharibacteria_bog_1338_contigs Prevotella_denticola_F0289 Candidatus_Saccharibacteria_RIFCSPHIGHO2_02_FULL_47_12_contigs Bacteroides_sp._D20 Candidatus_Saccharibacteria_DOLZORAL124_54_13_A_contigs Bacteroides_sp._4_1_36 Prevotella_denticola_CRIS_18C-A Candidatus_Saccharibacteria_AWTP1_31_contigs Bacteroides_uniformis_CAG:3 Prevotella_multiformis_DSM_16608 Candidatus_Saccharibacteria_SZUA_97_contigs Bacteroides_uniformis_strain_2789STDY5834844 Prevotella_histicola_JCM_15637 Prevotella_histicola_F0411 Candidatus_Saccharibacteria_SZUA_47_contigs Bacteroides_uniformis_strain_DSM_6597 Candidatus_Saccharibacteria_SZUA_30_contigs Bacteroides_fluxus_YIT_12057 Prevotella_sp._oral_taxon_306 Candidatus_Saccharibacteria_UBA6824UBA6824_contigs Prevotella_veroralis_F0319 Bacteroides_clarus_YIT_12056 Candidatus_Saccharibacteria_RIFCSPHIGHO2_12_FULL_47_17_contigs Bacteroides_clarus_CAG:160 Candidatus_Saccharibacteria_RIFCSPHIGHO2_12_FULL_47_16b_contigs Bacteroides_eggerthii_DSM_20697 Candidatus_Saccharibacteria_CG10_big_fil_rev_8_21_14_0_10_47_8CG10_big_fil_rev_8_21_14_0_10_47_8_contigs Prevotella_intermedia_strain_KCOM_1101 Bacteroides_eggerthii_1_2_48FAA Prevotella_intermedia_strain_WW414Prevotella_disiens_JCM_6334 Candidatus_Saccharibacteria_RIFCSPHIGHO2_12_FULL_48_21_contigs Bacteroides_eggerthii_CAG:109 Candidatus_Saccharibacteria_RIFCSPHIGHO2_01_FULL_49_21_contigs Bacteroides_clarus_YIT_12056 Candidatus_Saccharibacteria_UBA7683UBA7683_contigs Bacteroides_stercoris_strain_DSM_19555 Prevotella_disiens_DNF00882_contig001Prevotella_pallens_ATCC_700821 Bacteroides_stercoris_CAG:120 Candidatus_Saccharibacteria_RIFCSPHIGHO2_12_FULL_42_8_contigs

Bacteroides_stercoris_strain_CL09T03C01 Candidatus_Saccharibacteria_32_45_332_45_3_contigs

Bacteroides_reticulotermitis_JCM_10512 Candidatus_Saccharibacteria_INTACYC067_contigs Prevotella_nigrescens_ATCC_33563 Prevotella_micans_F0438 Bacteroides_luti_strain_DSM_26991 Candidatus_Saccharibacteria_Bin10_3_contigs Prevotella_nigrescens_strain_KCOM_1102_KB5_1_Prevotella_corporis_strain_MJR7716 Bacteroides_pyogenes_JCM_6292 Candidatus_Saccharibacteria_UBA5946UBA5946_contigs Bacteroides_caccae_CAG:21 Candidatus_Saccharibacteria_ME_46_23_contigs Prevotella_amnii_strain_DNF00307 Prevotella_amnii_CRIS_21A-A Bacteroides_thetaiotaomicron_CAG:40 candidate_division_TM7_genomosp_GTL1GTL1_contigs Bacteroides_sp._CAG:754 Prevotella_bivia_JCVIHMP010 Candidatus_Saccharibacteria_Co191P4bin22_contigs Prevotella_bivia_DSM_20514 Bacteroides_ovatus_CAG:22 Bacteroides_fragilis_strain_ATCC_25285 Candidatus_Saccharibacteria_Th196P4bin6_contigs Prevotella_oralis_ATCC_33269 Prevotella_oralis_HGA0225 Bacteroides_fragilis_CAG:47 Candidatus_Saccharibacteria_Emb289P3bin132_contigs Prevotella_sp._KH2C16 Prevotella_sp._P5-64 Bacteroides_fragilis_CAG:558 Candidatus_Saccharibacteria_Th196P3bin19_contigs Bacteroides_sp._3_2_5 Prevotella_sp._P4-67 Candidatus_Saccharibacteria_genomosp_TM7_H1E1_contigs Bacteroides_fragilis_str._3783N1-8 Candidatus_Saccharibacteria_UBA6433UBA6433_contigs Prevotella_sp._CAG:474 Bacteroides_pyogenes_JCM_10003 Prevotella_sp._P5-108 Bacteroides_graminisolvens_DSM_19988 Candidatus_Saccharibacteria_TM7_EAM_G5_1_HOT_356strain_TM7_EAM_G5_1_HOT_356_contigs Prevotella_sp._P4-51 Bacteroides_sp._HPS0048 Candidatus_Saccharibacteria_TM7_EAM_G5_2_HOT_356strain_TM7_EAM_G5_2_HOT_356_contigs Bacteroides_salyersiae_WAL_10018 Candidatus_Saccharibacteria_Nc150P3bin23_contigs Prevotella_sp._kh1p2 Bacteroides_sp._CAG:189 Bacteroides_nordii_CL02T12C05 Candidatus_Saccharibacteria_Nt197P3bin119_contigs Bacteroides_salyersiae_strain_2789STDY5608871 Prevotellaceae_bacterium_KH2P17 Candidatus_Saccharibacteria_MAG_RACS_012_contigs Bacteroides_sp._3_1_23 Prevotella_sp._BV3P1 Bacteroides_faecichinchillae_strain_DSM_26883 Candidatus_Saccharibacteria_MAG_RACS_017_contigs Bacteroides_finegoldii_strain_2789STDY5608840 Candidatus_Saccharibacteria_UBA3749UBA3749_contigs Bacteroides_finegoldii_CAG:203 G5 Prevotella_buccalis_DNF00853_contig01 Bacteroides_finegoldii_DSM_17565 Candidatus_Saccharibacteria_UBA2866UBA2866_contigs Bacteroides_caccae_ATCC_43185 Prevotella_buccalis_DNF00985_contig001 Bacteroides_sp._1_1_14 Candidatus_Saccharibacteria_TM7_G3_2_Rum_HOT_351Bstrain_TM7_G3_2_Rum_HOT_351B_contigs

Bacteroides_faecis_MAJ27 Prevotella_sp._oral_taxon_299 Candidatus_Saccharibacteria_UBA3218UBA3218_contigs Prevotella_timonensis_strain_UMB0818Prevotella_timonensis_CRIS_5C-B1 Bacteroides_sp._HMSC067B03 Prevotella_sp._HMSC073D09 Bacteroides_faecis_CAG:32 Candidatus_Saccharibacteria_UBA1235UBA1235_contigs Prevotella_sp._oral_taxon_317 Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides_sp._AR20 Candidatus_Saccharibacteria_UBA3829UBA3829_contigs Prevotella_sp._oral_taxon_472 Bacteroides_thetaiotaomicron_strain_NLAE-zl-C579 Bacteroides_sp._3_1_13 TM7_phylum_sp_oral_taxon_351strain_TM7_HOT_351_SAG3_contigs Prevotella_loescheii_DSM_19665 Bacteroides_sp._1_1_30 Bacteroides_sp._2_2_4 Prevotella_saccharolytica_F0055 Candidatus_Nanosyncoccus_FGB4_strain_JCVI_47_bin_30_contigs Prevotella_sp._885 Bacteroides_sp._HMSC073E02 Prevotella_marshii_DSM_16973 Bacteroides_sp._HMSC068A09 Prevotella_sp._CAG:520 Candidatus_Nanosyncoccus_FGB3_strain_JCVI_44_bin_1_contigs Bacteroides_sp._D1

Prevotella_sp._P4-65 Bacteroides_caecimuris_strain_I48 Prevotella_stercorea_DSM_18206Prevotella_stercorea_CAG:629 Bacteroides_xylanisolvens_XB1A Candidatus_Nanosyncoccus_FGB2_strain_JCVI_32_bin_36_contigs Prevotella_sp._P4-76 Bacteroides_xylanisolvens_SD_CC

Bacteroides_sp._D22 Prevotella_sp._P5-119 Candidatus_Saccharibacteria_TM7_KMM_G3_1_HOT_351strain_TM7_KMM_G3_1_HOT_351_contigs Prevotella_sp._P5-60 Bacteroides_sp._2_1_22 Bacteroides_sp._D2

Bacteroides_caccae_CL03T12C61 Prevotella_sp._P5-125 Bacteroides_ovatus_V975_genome_assembly Candidatus_Nanosyncoccus_GGB1_strain_JCVI_5_bin_8_contigs Prevotella_sp._109 Bacteroides_ovatus_strain_ATCC_8483

Bacteroidales_bacterium_KHT7

Paraprevotella_clara_YIT_11840 Prevotella_sp._CAG:592 Paraprevotella_clara_CAG:116 Candidatus_Nanosyncoccus_FGB1_strain_JCVI_1_bin_4_contigs Paraprevotella_xylaniphila_YIT_11841

Prevotella_sp._oral_taxon_473 Candidatus_Prevotellaceae_FGB1_strain_JCVI_11_bin.7

Candidatus_Prevotellaceae_FGB1_strain_JCVI_44_bin.38

Candidatus_Prevotellaceae_FGB2_strain_JCVI_24_bin.11 Prevotella_sp._CAG:255 Candidatus_Prevotellaceae_FGB2_strain_JCVI_32_bin.66 TM7_phylum_sp_oral_taxon_351strain_TM7_HOT_351_SAG4_contigs Candidatus_Prevotellaceae_FGB2_strain_JCVI_38_bin.21

Prevotella_sp._CAG:891 Prevotella_sp._CAG:5226

Prevotella_sp._CAG:755

Prevotella_sp._oral_taxon_302 Prevotella_sp._CAG:617

Prevotella_tannerae_ATCC_51259 Prevotella_sp._CAG:1185 Prevotella_sp._khp7 TM7_phylum_sp_oral_taxon_351strain_TM7_HOT_351_SAG2_contigs G3 Prevotella_sp._CAG:1124

Prevotella_sp._CAG:1058 Prevotella_sp._ne3005Prevotella_sp._tc2-28 Candidatus_Saccharibacteria_UBA1788UBA1788_contigs Prevotella_sp._lc2012 Prevotella_sp._khp1 Candidatus_Saccharibacteria_UBA3304UBA3304_contigs Candidatus_Saccharibacteria_UBA2834UBA2834_contigs Prevotella_ruminicola_23 Prevotella_sp._P3-92 Prevotella_sp._BP1-145

Prevotella_sp._BP1-148 Prevotella_sp._P4-119 Prevotella_sp._P4-98 Prevotella_sp._P3-120 Prevotella_sp._tf2-5 Candidatus_Saccharibacteria_UBA3723UBA3723_contigs Prevotella_sp._P5-50

Prevotella_aff._ruminicola_Tc2-24 Prevotella_sp._P5-126

Prevotella_sp._P5-92

Prevotella_sp._P2-180 Candidatus_Saccharibacteria_UBA3225UBA3225_contigs Candidatus_Saccharibacteria_UBA4387UBA4387_contigs Prevotella_ruminicola_strain_BPI-162 Candidatus_Saccharibacteria_Nt197P3bin109_contigs Prevotellaceae_bacterium_MN60 Candidatus_Saccharibacteria_Th196P3bin64_contigs Prevotellaceae_bacterium_HUN156 Candidatus_Saccharibacteria_Th196P3bin118_contigs Candidatus_Saccharibacteria_Emb289P1bin101_contigs Candidatus_Saccharibacteria_Th196P3bin140_contigs

Alloprevotella_tannerae_strain_JCVI_30_bin.15 Alloprevotella_tannerae_strain_JCVI_16_bin.13 Alloprevotella_tannerae_strain_JCVI_42_bin.12 Candidatus_Saccharibacteria_UBA949UBA949_contigs Candidatus_Saccharibacteria_Emb289P1bin99_contigs Candidatus_Saccharibacteria_Lab288P4bin92_contigs TM7_phylum_sp_oral_taxon_350strain_TM7_HOT_350_SAG1_contigs candidate_division_TM7_single_cell_isolate_TM7a_contigs Candidatus_Nanosynbacter_TM7c_strain_JCVI_32_bin_19_contigs Candidatus_Nanosynbacter_TM7c_strain_JCVI_1_bin_5_contigs

Desulfotomaculum copahuensis strain LMa1 LMA27_trimmed_contig_1 Candidatus_Nanosynbacter_TM7c_strain_JCVI_6_bin_10_contigs

Peptococcaceae bacterium SCADC1_2_3 isolate SCADC2 contig_1

Caldisalinibacter kiritimatiensis strain L21-TH-D2 NODE_40

Clostridiales bacterium 38-18 SCNpilot_bf_inoc_scaffold_0 Peptostreptococcaceae bacterium oral taxon 113 str. W5053 candidate_division_TM7_single_cell_isolate_TM7c_contigs Oxobacter pfennigii strain DSM 3222 OXPF_contig000001

Desulfotomaculum thermosubterraneum DSM 16057 Candidatus_Nanosynbacter_sp_TM7_MAG_III_A_2_strain_JCVI_32_bin_12_contigs

Proteiniborus ethanoligenes strain DSM 21650 Acidaminobacter hydrogenoformans DSM 2784

Caloranaerobacter azorensis H53214 contig1

Peptococcaceae bacterium SCADC1_2_3 contig_1

Desulfotomaculum geothermicum strain DSM 3669 Desulfotomaculum ferrireducens strain GSS09 chromosome Caloranaerobacter azorensis DSM 13643

Desulfotomaculum profundi strain Bs107 Contig_1010 Desulfotomaculum arcticum strain DSM 17038 Desulfotomaculum nigrificans CO-1-SRB chromosome Desulfotomaculum australicum DSM 11792 Candidatus_Saccharibacteria_TM7_ANC_3839_G1_1strain_TM7_ANC_G1_1_contigs

Desulfotomaculum kuznetsovii DSM 6115

Caloranaerobacter sp. TR13 contig1 Desulfotomaculum hydrothermale Lam5 WGS project data Candidatus Desulforudis audaxviator MP104C Syntrophomonas wolfei subsp. wolfei str. Goettingen G311 Garciella nitratireducens DSM 15102

Desulfotomaculum hydrothermale Lam5 = DSM 18033 Lutispora thermophila DSM 19022

Desulfotomaculum aeronauticum DSM 10349

Pelotomaculum thermopropionicum SI DNA Desulfotomaculum gibsoniae DSM 7213 Desulfotomaculum acetoxidans DSM 771 Clostridiales bacterium KA00134 TM7_phylum_sp_oral_taxon_346strain_TM7_HOT_346_SAG2_contigs

Fusibacter sp. 3D3 DNA Proteiniborus sp. DW1 Candidatus_Nanosynbacter_sp_TM7_MAG_III_A_2_strain_JCVI_6_bin_12_contigs Desulfotomaculum ruminis DSM 2154 Desulfotomaculum reducens MI-1

Desulfotomaculum putei DSM 12395

Heliobacterium modesticaldum Ice1 strainDesulfonispora Ice1 thiosulfatigenesSyntrophothermus DSM 11270 lipocalidus DSM 12680

Desulfosporosinus sp. HMP52 Desulfosporosinus_HMP51_contig_1 Carboxydocella sporoproducens DSM 16521 TM7_phylum_sp_oral_taxon_346strain_TM7_HOT_346_SAG3_contigs Desulfosporosinus youngiae DSM 17734 chromosome

Thermincola ferriacetica strain Z-0001 Tfer_ctg01

Dethiobacter alkaliphilus AHT 1 ctg20 Syntrophomonas zehnderi OL-4 TM7c Desulfosporosinus sp. Tol-M Desulfosporosinus_sp._Tol-M_Contig_10 Desulfosporosinus acididurans strain M1 DEAC_contig000001 Candidatus_Saccharibacteria_TM7_G1_3_12Astrain_TM7_G1_3_12A_contigs

Thermincola potens JR chromosome ThermotaleaAN619_contig000008 metallivorans strain B2-1 Clostridium caminithermale DSM 15212 Geosporobacter subterraneus DSM 17957 Alkaliphilus peptidifermentans DSM 18978

Geosporobacter ferrireducens strain IRF9 chromosome Anaeromicrobium sediminis strain DY2726D Seq1 Clostridium halophilum strain M1

Caminicella sporogenes DSM 14501

Alkaliphilus oremlandii OhILAs Tindallia californiensis strain APO Carboxydocella sp. CarboxydocellaJDF658 DNA sp. ULO1 DNA Tindallia magadiensis strain Z-7934 Alkaliphilus metalliredigens QYMF Natronincola ferrireducens strain DSM 18346

Desulfosporosinus lacus DSM 15449 Natronincola peptidivorans strain DSM 18979

Anaerovirgula multivorans strain SCA Clostridium formicaceticum strain DSM 92 chromosome

Clostridium formicaceticum strainATCC 27076 Clostridium aceticum strain DSM 1496 contig_1 Candidatus_Nanosynbacteraceae_FGB2_strain_JCVI_32_bin_44_contigs Desulfosporosinus meridiei DSM 13257 Clostridium aceticum strain DSM 1496 Desulfosporosinus hippei DSM 8344 [Clostridium] thermoalcaliphilum strain DSM 7309 CLOTH_contig000001 [Clostridium] paradoxum JW-YL-7 = DSM 7308 strain JW-YL-7 ctg1 Desulfosporosinus sp. OT TOU.assembly.9 Peptoclostridium acidaminophilum DSM 3953 chromosome

Peptoclostridium litorale DSM 5388 strain W6 plasmid CLIT_20p Desulfosporosinus sp. BG contig00001 [Clostridium] litorale DSM 5388 Dehalobacter sp. TeCB1 NODE_1162_length_1484_cov_562.259_ID_211506 Desulfosporosinus orientis DSM 765 Clostridium sticklandii str. DSM 519 chromosome

Peptococcaceae bacterium CEB3 CEB3_contig000001 Eubacterium yurii subsp. margaretiaeATCC 43715

Peptostreptococcaceae bacteriumAS15 ctg120005099211 [Eubacterium] yurii strainATCC 43714 TM7_phylum_sp_oral_taxon_346strain_TM7_HOT_346_SAG1_contigs B Candidatus_Peptostreptococcaceae_FGB1_strain_JCVI_44_bin.10 Peptoanaerobacter stomatis strain OBRC8 ctg120007290659

Eubacteriaceae bacterium CM2

Clostridium hiranonis DSM 13275 Scfld14 Peptostreptococcus russellii strain Calf135 Desulfosporosinus sp. OL contig00001 Peptostreptococcus anaerobius CAG:621 Desulfitobacterium chlororespirans DSM 11544 Peptostreptococcus anaerobius strain KA00810

Desulfosporosinus acidiphilus SJ4 Peptostreptococcus anaerobius VPI 4330 Candidatus_Saccharimonas_spbin_8_contigs Desulfitobacterium dichloroeliminans LMG P-21439 Peptostreptococcus sp. MV1 contig001 Desulfosporosinus sp. I2 contig00001 Peptostreptococcus sp. D1 Desulfitobacterium dehalogenans ATCC 51507 Candidatus_Peptostreptococcus_GGB1_strain_JCVI_1_bin.2

Candidatus_Peptostreptococcus_GGB1_strain_JCVI_32_bin.13

Desulfitobacterium metallireducens DSM 15288 Candidatus_Peptostreptococcus_GGB1_strain_JCVI_44_bin.26 Peptostreptococcus stomatis DSM 17678 contig00005 TM7_phylum_sp_oral_taxon_349strain_TM7_HOT_349_SAG1_contigs Candidatus_Peptostreptococcus_GGB1_strain_JCVI_6_bin.6 Desulfitobacterium hafniense DCB-2 Candidatus_Peptostreptococcus_GGB1_strain_JCVI_25_bin.6

Candidatus_Peptostreptococcus_GGB1_strain_JCVI_24_bin.7

Candidatus_Peptostreptococcus_GGB1_strain_JCVI_42_bin.2 Candidatus_Peptostreptococcus_GGB1_strain_JCVI_12_bin.18 Candidatus_Nanosynbacter_GGB2_strain_JCVI_32_bin_57_contigs Terrisporobacter othiniensis strain 08-306576 Contig001

Terrisporobacter glycolicus strain KPPR-9 Dehalobacter sp. UNSWDHB Contig_1 Gracilibacter sp. BRH_c7a BRHa_1000097Dehalobacter restrictus DSM 9455 Clostridium sp. 1_1_41A1FAA Sulfobacillus thermosulfidooxidans strain ZBY contig1 Clostridium bartlettii CAG:1329 Intestinibacter bartlettii strain 2789STDY5834879 Candidatus_Saccharimonas_spbin_10_contigs Syntrophobotulus glycolicus DSM 8271 Clostridium bartlettii DSM 16795 Scfld_02_17 Symbiobacterium thermophilum isolate G2 contig00001 Romboutsia lituseburensis DSM 797 Paraclostridium benzoelyticum strain JC272 Contig1 Sulfobacillus acidophilus DSM 10332 Symbiobacterium thermophilum IAM 14863 DNA [Clostridium] sordellii Thermaerobacter subterraneus DSM 13965 Paraclostridium benzoelyticum strain JC302 ctg7180000005295 TM7_phylum_sp_oral_taxon_955strain_PM004_contigs Paraclostridium bifermentans ATCC 19299 gcdATCC19299.contig.0

Paraclostridium bifermentans ATCC 638 gcdATCC638.contig.0

Sulfobacillus acidophilus TPY Clostridium sp. NCR contig00001 Peptococcaceae bacterium 1109 scaffold00001 Thermaerobacter marianensis DSM 12885 Paeniclostridium sordellii ATCC 9714 gcs9714.contig.0 Candidatus_Saccharibacteria_UBA1944UBA1944_contigs Clostridiales bacterium PH28_bin88 ph28_1008 Clostridium sp. HMSC19A11

Clostridium sp. HMSC19B01

Desulfitibacter sp. BRH_c19 BRHa_1000314 Clostridium sp. HMSC19C08 Clostridioides difficile strain CD51 Candidatus_Saccharibacteria_INTAAUR015_contigs Clostridium sp. HMSC19B12

Clostridium sp. HMSC19D07

Peptococcus niger strain DSM 20475 Clostridioides difficile strain VRECD0026 Clostridium sp. HMSC19E03 Candidatus_Saccharibacteria_UBA669UBA669_contigs Clostridium sp. HMSC19D02

Clostridium sp. HMSC19C09 82 124 Clostridium sp. HMSC19B11 6 10 Candidatus_Saccharibacteria_32_50_1032_50_10_contigs Clostridium sp. HMSC19B10 Pseudoclostridium thermosuccinogenes strain DSM 5808 NODE_100_length_5569_cov_91.1003_ID_15429 Clostridium sp. CAG:715 Clostridium sp. HMSC19B04 Clostridium sp. Bc-iso-3 Bc-iso-3_contig01 Clostridium sp. CAG:967 Pseudobacteroides cellulosolvens ATCC 35603 = DSM 2933[Clostridium] ctg1 straminisolvens JCM 21531 DNA Clostridium sp. HMSC19C05 U_CONTIG04 Pseudoclostridium thermosuccinogenes strain DSM 5809 scaffold1_size3002637_cov202.5430 Clostridium sp. CAG:729 Clostridium sp. HMSC19C11 Candidatus_Saccharibacteria_UBA6223UBA6223_contigs Caloramator quimbayensis strain USBA 833 Ruminiclostridium thermocellum DSM 2360 Clostridium sp. CAG:768 [Clostridium] clariflavum DSM 19732 chromosome Fervidicella metallireducens AeB contig00001 is strain ML2 Ruminiclostridium thermocellum strain LQRI Clostridium sp. CAG:813 U SFBNY Herbivorax saccincola strain GGR1 chromosome Clostridium cylindrosporum DSM 605 CLCY_10c Clostridium sp. CAG:306 Candidatus_Saccharibacteria_UBA6258UBA6258_contigs umin Caloramator australicus RC3 WGS project CAKP00000000 data RuminiclostridiumRuminiclostridium cellobioparum hungatei subsp. strain termitidis DSM CT1112 14427 CLHUN_contig000001 Ct_contig00001 Ruminiclostridium papyrosolvens DSM 2782 ctg35 Caloramator mitchellensis strain VF08 ABG79_contig000001 B-3 SFB3_440 F Thermobrachium celere DSM 8 4_355 Candidatus_Saccharimonas_aalborgensisTM71_contigs Ruminiclostridium papyrosolvens C7 contig00001 Caloramator proteoclasticus DSM FB sp. S Youngiibacter fragilis 232.1 contig_99 tus Arthromitus sp. SFB-turkey isolate UMNCA01 16S_rRNA_consensus SFBSU_009 Proteiniclasticum r da roteiniclasticum ruminis strain CGMCC 1.5058 tus sp. SFB-mouse-NY Candidatus_Saccharibacteria_UBA1932UBA1932_contigs [Clostridium] cellulolyticum H10 chromosome P mi [Clostridium] stercorarium subsp. stercorarium DSM 8532 chromosome Candi e-Yit DNA Candidatus Arthromitus sp. SFB-rat-Yit DNA us [Butyribacterium] methylotrophicum strain DSM 3468 BUME_contig000001 Candidatus_Saccharibacteria_UBA1949UBA1949_contigs [Clostridium] stercorarium subsp. leptospartum DSM 9219 Candidatus Arthromitus sp. SFB-2 SFB2_329

Candidatus Arthromitus SFB-mo ndidatus Arthro Clostridium sp. BNL1100 p. Ca s Candidatus_Saccharibacteria_SZUA_359_contigs datus Arthromitus sp. rthromitusSFB-4 S sp. SFB-mouse-NL Candidatus diArthromitus sp. SFB-5 A SFB5_338

Can romitus h Candidatus Arthromitus sp. SFB-1 SFB1_367 Candidatus_Saccharibacteria_DOLZORAL124_55_12_contigs Caldicoprobacter faecalis strain DSM 20678 3C Candidatus N yticum strain DSM 21864 Candidatus Arthromitus sp. SFB-mouse-SU DSM 2631 Eubacterium callanderi strain NLAE-zl-G225 in 91 Candidatus_Saccharibacteria_DOLZORAL124_45_3_contigs Candidatus Art ium sp. amylol Clostridium oryzae strain DSM 28571 CLORY_contig000001 Eubacterium limosum strain ATCC 8486 chromosome lax stra SM 61 Clostrid tridium os le D Candidatus_Saccharibacteria_UBA6573UBA6573_contigs Eubacterium maltosivorans strain YI HybridContig12 Cl omosome tina Acetobacterium wieringae strain DSM 1911 ACWI_ EubacteriumEubacterium callanderi strain callanderi KIST612 strain FD chr Clostridium frigidicarnis strain DSMtes 12271 Clostridium fal strain FORC_025 Candidatus_Saccharibacteria_UBA2952UBA2952_contigs ns ostridium intestinaleidium in URNW e Cl tr los C Eubacterium barkeri 0001 Candidatus_Saccharibacteria_UBA6575UBA6575_contigs Clostridium ventriculi strain 2789STDY5834858 ntig00001 Acetobacterium bakii strainEubac DSM 8239 contig_1 tig0 o Clostridium cadaveris strain NLAE-zl-G419 con terium aggregans strain SR12 Clostridium perfring S. aal Candidatus_Saccharibacteria_UBA2018UBA2018_contigs Anaerofustis stercorihominis DSM 17244 Scfld_02_4 sp. C8 G1 Pseudoramibacter alactolyticus ATCC 23263 Clostridium cavendishii DSM 21758 AA strain VPI 5359 lostridium chauvoei strain DSM 7528 C agoforme AAU1 c Acetobacterium woodii DSM 1030 stridium Candidatus_Clostridiales_FGB1_strain_JCVI_32_bin.60 sart _2_43F Candidatus_Saccharibacteria_UBA1050UBA1050_contigs Clo m strain 2789STDY5834856 Alkalibacter saccharofermentans DSM 14828 m iu Candidatus_Clostridiales_FGB2_strain_JCVI_12_bin.17 sp. 7 contig000001 Clostridium chauvoei strain 12S0467poricu Clostrid mosome Candidatus_Saccharibacteria_UBA6664UBA6664_contigs Clostridium

Clostridium dis 21 2 272 Candidatus_Saccharibacteria_UBA8500_contigs LLY_N11 12chro Clostridium disporicum strain 2789STDY5608827 n . CAG: p Clostridium celatum DSM 1785 tridium sp.m CAG:265 s os Candidatus_Saccharibacteria_UBA2112UBA2112_contigs Cl Cl ostridium sp. CAG:440 Clostridiu Clostridium sp. CAG:343 Clostridium sp. DSM 8431 Candidatus_Saccharibacteria_UBA10027_contigs Clostridium sp. CAG:356 Clostridium perfringens strai stridium gasigenes strain DSM Clostridium sp. CAG:269 1 Clo Candidatus_Saccharibacteria_32_50_1332_50_13_contigs Clostridium sp. CAG:389 some Clostridiumidium colicanis thermobutyricum 209318 DSM 4928 CLTH_contig000001 tr Clostridium sp. CAG:780 Clos Candidatus_Saccharibacteria_RIFCSPHIGHO2_12_FULL_47_16_contigs Clostridium sp. CAG:354 6D1 chromo Clostridium baratii strain 2789STDY5834907 JKY Clostridium sp. CAG:492 lostridium baratii str. Sullivan C in Clostridium sp. CAG:508 Candidatus_Saccharibacteria_RIFCSPHIGHO2_12_FULL_44_22_contigs Clostridium paraputrificum strain 2789STDY5834857 62F_CONTIG1 Clostridium sp. CAG:567 Clostridium paraputrificum strain 373-A1 CP373A1_1 butyricum stra BUN lostridium uliginosum strain DSM 12992 Clostridium sp. CAG:273 C Candidatus_Nanosynbacter_UMGS1926_strain_JCVI_1_bin_14_contigs ostridium . IBUN125C2F ClosIBUN125C_CONTIG1 ClosI Candidatus_Clostridiales_FGB3_strain_JCVI_32_bin.9Clostridium sp. CAG:571 Cl sp ium Clostridium sp. CAG:452 Clostridiumrid sp. IBUN22Ap. IBUN6 ClosIBUN22A_CONTIG1 TM7_phylum_sp_oral_taxon_352strain_TM7_HOT_352_SAG7_contigs IBUN13A ClosIBUN13A_CONTIG1 Clostridium sp. CAG:1219 Clost sp. A005 Cneo_1 Clostridium sp. CAG:921 Clostridium s Candidatus_Saccharibacteria_UMGS1877_contigs Clostridium

Clostridium butyricum E4 str. BoNT E BL5262 plasmid pCLP Clostridium sp. CAG:451 TM7_phylum_sp_oral_taxon_352strain_TM7_HOT_352_SAG2_contigs Clostridium sp. HMSC19A10 -4(HMT) Clostridium sp. CAG:417 ridium neonatale strain LCDC99A006icum DSMCneo_1 13864 2619 CLPUN_contig000001 M Clost Clostridium sp. CAG:628 onicum N1 Candidatus_Saccharibacteria_UMGS1986_contigs t Clostridium neonatale strain LCDC99strain DS ridium saccharobutylicum DSM 13864 contig_1 Clostridiu utylace lost C C Candidatus_Saccharibacteria_UMGS1805_contigs lostridium sp.m CAG:433sp. CAG:762 Clostridium saccharobutyl Clostridium sp. CAG:302 Clostridium puniceum ome tridium saccharoperb CLOBL_contig000001 _1 EubacteriumClostridium dolichum sp.CAG:375 CAG:524 8 g Candidatus_Nanosynbacter_GGB3_strain_JCVI_36_bin_4_contigs Clos chromos Clostridium sp. HGF2 contig00005 Clostridiales bacterium CHKCI006 isolate CHKC6 Clostridium saccharoperbutylacetonicum strain N1-504 chromosome MBC34-26 conti Candidatus_Saccharibacteria_UMGS2061_contigs Clostridium sp. BL- Eubacterium sp. 3_1_31 Clostridium sp. DL-VIII Candidatus_Saccharibacteria_UMGS1848_contigs Clostridium beijerinckii ATCC 35702 Clostridium sp. CAG:307 Clostridium sp. Maddingley Streptococcus mutans ATCC 25175 Contig001 Candidatus_Saccharibacteria_UMGS1831_contigs Clostridium sp. CAG:288 Clostridium chromiireducens strain DSM 23318 CLCHR_contig000001 Clostridium sp. CAG:568 Clostridium beijerinckii strain NRRL B-593 CLOBI_contig000001 Candidatus_Nanosynbacter_GGB1_strain_JCVI_3_bin_14_contigs Streptococcus mutans 1SM1 contig1 Clostridium diolis strain NJP7 scaffold1 Clostridium grantii DSM 8605 Candidatus_Nanosynbacter_GGB4_strain_JCVI_6_bin_3_contigs Clostridium collagenovorans DSM 3089 Clostridium sulfidigenes strain 113A c1 TM7_phylum_sp_oral_taxon_952strain_TM7x_contigs Clostridium sp. BL8 Contig01 Clostridium argentinense CDC 2741 U732.Contig233 TM7_phylum_sp_oral_taxon_353strain_TM7_HOT_353_SAG1_contigs Clostridium argentinense strain 89G chromosome Clostridium sp. USBA 49 TM7_phylum_sp_oral_taxon_488strain_AC001_contigs Clostridiales bacterium oral taxon 876 str. F0540 Clostridium tepidiprofundi DSM 19306 CLTE_contig000001 Candidatus_Nanosynbacteraceae_FGB1_strain_JCVI_32_bin_22_contigs

Clostridiumum colicanis novyi A DSM str. NCTC13634 538CLCO_contig000001 plasmid p1Cn538 Clostridi TM7_phylum_sp_oral_taxon_957strain_BB001_contigs Clostridium homopropionicum strain DSM 5847 TM7x Candidatus_Saccharibacteria_DOLZORAL124_45_28_contigs Clostridium homopropionicum DSM 5847 CLHOM_contig000001 Clostridium haemolyticum NCTC 9693 plasmid p1Ch9693 Candidatus_Saccharibacteria_INTACYC018_contigs Clostridium botulinum D str. 1873 plasmid pCLG1 Clostridium sp. K25 plasmid p1K25 Candidatus_Saccharibacteria_UBA6209UBA6209_contigs Clostridium novyi B str. ATCC 27606 plasmid p2Cn27606 Clostridium haemolyticum strain KFSHRC_CH1 c1 Candidatus_Saccharibacteria_INTACYC070_contigs Clostridium sp. L74 contig00001 Clostridium tepidum strain PE scaffold_0 Candidatus_Saccharibacteria_32_49_1032_49_10_contigs Clostridium tepidum strain IEH 97212 scaffold_0 Clostridium sporogenes strain 8-O scaffold_1 candidate_division_TM7_JGI_0001002_L20strain_JGI_0001002_L20_contigs Clostridium sporogenes isolate 1990 VT94_contig001 Candidatus_Saccharibacteria_UBA4727UBA4727_contigs Clostridium botulinum A str. ATCC 3502 complete Clostridium combesii strain DSM 20696 scaffold_0 Candidatus_Saccharibacteria_UBA6039UBA6039_contigs Clostridium acetireducens DSM 10703 CLAC_contig000001 Clostridium proteolyticum DSM 3090 Candidatus_Saccharibacteria_UBA4663UBA4663_contigs Pseudobutyrivibrio sp. YE44 Clostridium sp. HMP27 Clostridium-HMP27_contig_1 Butyrivibrio fibrisolvens 16/4 draft Clostridium tetanomorphum DSM 665 contig1 Candidatus_Saccharibacteria_CG2_30_41_52CG2_30_41_52_contigs Pseudobutyrivibrio ruminis strain JK626 contig000001 Clostridium tetani strain 184.08 Scaffold1.1 Pseudobutyrivibrio sp. ACV-2 Clostridium cochlearium strain NCTC13027 Candidatus_Saccharibacteria_HGW_Saccharibacteria_1HGW_Saccharibacteria_1_contigs Pseudobutyrivibrio sp. NOR37 Clostridium tetani strain C2 plasmid pCTETC2 CtetC2_contig_27 Candidatus_Saccharibacteria_UBA4215UBA4215_contigs Clostridium cochlearium strain NLAE-zl-C224 PseudobutyrivibrioPseudobutyrivibrio xylanivorans DSM sp. 14809 AR14 Clostridium bornimense replicon M2/40_rep1 Candidatus_Saccharibacteria_UBA6040UBA6040_contigs Clostridium cellulovorans 743B Pseudobutyrivibrio xylanivoransPseudobutyrivibrio strain DSM sp. UC122510317 Clostridium pasteurianum DSM 525 = ATCC 6013 Candidatus_Saccharibacteria_UBA6175UBA6175_contigs Clostridium pasteurianum BC1 Pseudobutyrivibrio sp. 49 Clostridium acidisoli DSM 12555 Candidatus_Saccharibacteria_UBA892UBA892_contigs Pseudobutyrivibrio sp. C4 Clostridium sp. DMHC 10 contig_1 Pseudobutyrivibrio sp. JW11 Candidatus_Saccharibacteria_49_2049_20_contigs Pseudobutyrivibrio ruminis strain ACV-9 Clostridium sp. CT7 contig.1 Clostridium roseum strain DSM 6424 CLROS_contig000001 Candidatus_Saccharibacteria_47_8747_87_contigs Pseudobutyrivibrio sp. OR37 Clostridium acetobutylicum EA 2018 Lachnospiraceae bacterium XBB2008 Clostridium acetobutylicum ATCC 824 Candidatus_Saccharibacteria_UBA8109_contigs Lachnospiraceae bacterium C10 Clostridium roseum strain DSM 7320 CROST_contig000001 Lachnospiraceae bacterium KHCPX20 Candidatus_Saccharibacteria_CG_2015_01t_48_29_contigs Clostridium aurantibutyricum strain DSM 793 CLAUR_contig000001 Lachnospiraceae bacterium A10 Clostridium felsineum DSM 794 CLFE_contig000001 Lachnospiraceae bacterium XBD2001 Candidatus_Saccharibacteria_SZUA_572_contigs Shuttleworthia sp. MSX8B ctg7180000006402 Clostridium magnum DSM 2767 Eubacterium ramulus strain 2789STDY5608891 Clostridium magnum DSM 2767 CLMAG_contig000001 Candidatus_Saccharibacteria_32_49_1232_49_12_contigs Clostridium scatologenes strain ATCC 25775

Clostridium carboxidivorans P7 ctg00276 Candidatus_Saccharibacteria_Th196P3bin58_contigs Roseburia sp. CAG:50 Eubacterium ramulus ATCC 29099 Clostridium carboxidivorans P7 Candidatus_Saccharibacteria_INTAAUR008_contigs Clostridium sp. SY8519 DNA Clostridium tyrobutyricum strain W428 chromosome Eubacterium oxidoreducens strain DSM 3217 Clostridium tyrobutyricum DIVETGP WGS project CBXI000000000 data Candidatus_Saccharibacteria_TM7_CMJM_G6_1_HOT_870strain_TM7_CMJM_G6_1_HOT_870_contigs Acetitomaculum ruminis DSM 5522 Clostridium kluyveri NBRC 12016 DNA

Lachnospiraceae bacterium A2 Clostridium kluyveri DSM 555 Candidatus_Saccharimonas_spbin_9_contigs Clostridium ljungdahlii strain ERI-2 scaffold1 Eubacterium sp. 14-2 Candidatus_Saccharimonas_sp_strain_JCVI_32_bin_49 Clostridium coskatii strain PS02 scaffold1 Lachnospiraceae bacterium 3-1 Clostridium coskatii strain PTA-10522 CLCOS_contig000001 Roseburia sp. 499 contig000001 Candidatus_Nanogingivalaceae_FGB1_strain_JCVI_1_bin_12_contigs Clostridium ragsdalei P11 CLRAG_contig000001 Roseburia sp. CAG:18 Roseburia faecis strain 2789STDY5608863 Clostridium autoethanogenum strain JA1-1 scaffold1 Candidatus_Nanogingivalaceae_FGB1_strain_JCVI_32_bin_33_contigs Clostridium ljungdahlii DSM 13528 strain PETC scaffold1 Roseburia faecis Candidatus_Nanogingivalaceae_FGB1_strain_JCVI_27_bin_3_contigs Clostridium autoethanogenum DSM 10061 Roseburia sp. CAG:197 Clostridiales bacterium KA00274 Lachnobacterium bovis DSM 14045 Candidatus_Nanogingivalaceae_FGB1_strain_JCVI_28_bin_11_contigs Mageeibacillus indolicus 0009-5 strain S7-24-11 contig01 Lachnobacterium bovis strain S1b Mageeibacillus indolicus UPII9-5 chromosome Lachnospiraceae bacterium C7 Ruminococcaceae bacterium KH2T8 Agathobacter rectalis strain 2789STDY5834884 Ruminococcaceae bacterium strain KHP2 Roseburia sp. CAG:45 Ruminococcaceae bacterium YAD3003 G6 Agathobacter ruminis strain JK623 contig000001 Ruminococcaceae bacterium YRB3002 Eubacterium rectale CAG:36 Candidatus_Clostridiales_FGB4_strain_JCVI_44_bin.37 Agathobacter rectalis strain 2789STDY5834968 Eubacterium brachy ATCC 33089

Roseburia sp. CAG:182 Eubacterium saphenum ATCC 49989

Roseburia sp. 831b contig000001 Clostridiales bacterium S5-A14a contig01

Roseburia inulinivorans CAG:15 Eubacterium sulci ATCC 35585 ctg7180000003427

Roseburia inulinivorans strain 2789STDY5608887 Eubacterium sulci ATCC 35585 Roseburia inulinivorans DSM 16841 R_inulinivorans-1.0.1_Cont604.1 Eubacterium infirmum F0142

Roseburia intestinalis XB6B4 draft Eubacterium sp. 68-3-10 unitig_0:quiver

Roseburia intestinalis CAG:13 Eubacterium pyruvativorans strain KHGC13

Roseburia intestinalis M50/1 draft Eubacterium pyruvativorans strain KHPC4

Roseburia hominis strain 2789STDY5608834 Mogibac terium pumilum s train ATCC 700696

Roseburia hominis A2-183 Mogibacterium timidum ATCC 33093 ctg7180000004146 Mogibacterium sp. CM50 ctg120007703401 Eubacterium plexicaudatum ASF492 Clostridium sp. CAG:349 Candidatus_Lachnospiraceae_FGB2_strain_JCVI_24_bin.14 Faecalibacterium sp. CAG:1138 Candidatus_Lachnospiraceae_FGB2_strain_JCVI_25_bin.13 Faecalibacterium sp. CAG:74 Candidatus_Lachnospiraceae_FGB2_strain_JCVI_8_bin.5 Faecalibacterium sp. CAG:74_58_120 Ley3_66761_scaffold_10055 Candidatus_Lachnospiraceae_FGB2_strain_JCVI_30_bin.4 Clostridiales bacterium strain WTE2008 Candidatus_Lachnospiraceae_FGB2_strain_JCVI_13_bin.1 Clostridiales bacterium strain R-7

Candidatus_Lachnospiraceae_FGB2_strain_JCVI_33_bin.3 Clostridium sp. CAG:1024

Candidatus_Lachnospiraceae_FGB2_strain_JCVI_19_bin.7 Clostridium sp. CAG:226

Candidatus_Lachnospiraceae_FGB2_strain_JCVI_42_bin.6 Clostridium sp. CAG:138

Candidatus_Lachnospiraceae_FGB2_strain_JCVI_23_bin.1 Subdoligranulum sp. CAG:314

Candidatus_Lachnospiraceae_FGB2_strain_JCVI_32_bin.8 Christensenella minuta strain DSM 22607

Catabacter hongkongensis strain HKU16 2806ref_2ab_c1 Candidatus_Lachnospiraceae_FGB2_strain_JCVI_10_bin.5 Christensenella minuta strain DSM 22607 scaffold_0 Candidatus_Lachnospiraceae_FGB2_strain_JCVI_48_bin.12 Catabacter hongkongensis strain ABBA15k Contig_1 Candidatus_Lachnospiraceae_FGB2_strain_JCVI_6_bin.2 Lachnospiraceae bacterium NK3A20 Monoglobus pectinilyticus strain 14 chromosome Sarcina sp. DSM 11001 Clostridiales Clostridium sp. CAG:448

Butyrivibrio hungatei DSM 14810 Anaerotruncus sp. CAG:390 Butyrivibrio sp. INlla18 Ruminococcus sp. CAG:382

Eubacterium sp. CAG:841 Butyrivibrio hungatei strain MB2003 chromosome I Butyrivibrio sp. INlla14 Ruminococcus sp. CAG:724

Butyricicoccus porcorum strain BB10 BB10_c1 Butyrivibrio proteoclasticus B316 chromosome 1 Butyrivibrio sp. INlla21 Butyricicoccus pullicaecorum 1.2

Butyrivibrio sp. M55 Butyricicoccus pullicaecorum DSM 23266 Butyrivibrio sp. YAB3001 Tree scale: 0.1 Papillibacter cinnamivorans DSM 12816 Butyrivibrio sp. Su6 Sporobacter termitidis DSM 10068

Oscillibacter sp. CAG:241 Butyrivibrio proteoclasticus strain P18 Butyrivibrio sp. INlla16 Oscillibacter valericigenes Sjm18-20 DNA

Butyrivibrio sp. ob235 Oscillibacter sp. 1-3

Oscillibacter sp. CAG:155 Butyrivibrio fibrisolvens DSM 3071 Butyrivibrio sp. TB Oscillibacter sp. PC13

Oscillibacter sp. KLE 1745

Lachnospiraceae bacterium strain KH1P17 Oscillibacter sp. KLE 1728 Lachnospiraceae bacterium KH1T2 Flavonifractor sp. An100 An100_contig_1

Lachnospiraceae bacterium XPB1003 Pseudoflavonifractor sp. An184 An184_contig_1

Lachnospiraceae bacterium NLAE-zl-G231 Leaves Ruminococcaceae bacterium D16 Pseudoflavonifractor sp. An85 An85_contig_1 Lachnospiraceae bacterium 3_1_57FAA_CT1 Fusicatenibacter sp. 2789STDY5834925 Pseudoflavonifractor sp. An44 An44_contig_1 Pseudoflavonifractor sp. An187 An187_contig_1

Eisenbergiella tayi strain NML120146 BEI63_contig000001 Pseudoflavonifractor sp. An176 An176_contig_1 Clostridium sp. KLE 1755 Flavonifractor sp. An135 An135_contig_1 Eisenbergiella tayi strain NML120147 BEI64_contig000001 Acetatifactor muris isolate GP69 Flavonifractor sp. An92 An92_contig_1

Lachnospiraceae bacterium 28-4 Pseudoflavonifractor capillosus ATCC 29799 B_capillosus-2.0.1_Cont402 Clostridium sp. CAG:510 Intestinimonas butyriciproducens strain AF211

Lachnospiraceae bacterium G11 Intestinimonas butyriciproducens strain 27-5-10 unitig_0 Flavonifractor sp. An10 An10_contig_1 LachnospiraceaeClostridium bacterium sp.YSD2013 CAG:91 GGBs Clostridium sp. ATCC BAA-442 Roseburia sp. CAG:100 Lachnospiraceae bacterium 7_1_58FAA

Flavonifractor plautii ATCC 29863

Flavonifractor plautii strain 2789STDY5834932 Lachnospiraceae bacterium COE1 Flavonifractor sp. An306 An306_contig_1 Roseburia sp. CAG:10041_57 Ley3_66761_scaffold_10235Lachnospiraceae bacterium A4 Flavonifractor sp. An9 An9_contig_1 Lachnospiraceae bacterium G41 Flavonifractor sp. An82 An82_contig_1 [Eubacterium] hallii isolate EH1 Eubacterium hallii CAG:12 Flavonifractor sp. An4 An4_contig_1

Flavonifractor sp. An112 An112_contig_1

Eubacterium sp. CAG:146 Flavonifractor sp. An91 An91_contig_1 [Eubacterium] hallii strain 2789STDY5834966 FGBs Flavonifractor sp. An52 An52_contig_1

Eubacterium sp. An3 An3_contig_1 Anaerofilum sp. An201 An201_contig_1

Eubacterium sp. An11 An11_contig_1 Ruthenibacterium lactatiformans strain 668 contig00001

Subdoligranulum sp. 4_3_54A2FAA

Ruthenibacterium lactatiformans strain 585-1 contig00001 Eubacteriaceae bacterium CHKCI004 isolate CHKC4 Anaerostipes Lachnospiraceaehadrus strain 2789STDY5834860 bacterium CAG:25 Gemmiger sp. An120 An120_contig_1

Clostridium sp. SS2/1 Scfld_03_33 Gemmiger sp. An87 An87_contig_1 Anaerostipes hadrus draft Gemmiger sp. An50 An50_contig_1 Anaerostipes sp. CAG:276 Gemmiger sp. An194 An194_contig_1

Gemmiger formicilis strain ATCC 27749

Subdoligranulum variabile DSM 15176 Anaerostipes caccae DSM Clostridium14662 Scfld_03_25 sp. CAG:122 Faecalibacterium prausnitzii L2/6 draft Clostridium sp. CAG:253 Lachnospiraceae bacterium TF01-11 TF01-11.Scaf1 Faecalibacterium sp. CAG:82 Clostridium sp. CAG:230 Faecalibacterium prausnitzii A2-165 Clostridium sp. CAG:75 Faecalibacterium sp. An121 An121_contig_1 Roseburia sp. CAG:380 Faecalibacterium sp. An58 An58_contig_1 Clostridium sp. CAG:277 Faecalibacterium sp. An122 An122_contig_1 Clostridium sp. CAG:62 Faecalibacterium sp. An192 An192_contig_1 Roseburia sp. CAG:309 Faecalibacterium sp. An77 An77_contig_1

Clostridium sp. CAG:167 Eubacterium coprostanoligenes strain ATCC 51222

Clostridium sp. CAG:217

Eubacterium sp. CAG:161 Clostridium sp. CAG:678

Eubacterium sp. CAG:192 Eubacterium sp. CAG:251 Eubacterium ventriosum ATCC 27560 Scfld0226 Eubacterium sp. CAG:156 Anaerotruncus sp. CAG:528 Eubacterium sp. CAG:180

Coprococcus eutactus CAG:665 Ruminococcus sp. CAG:563

Coprococcus sp. ART55/1 draft Ruminococcus sp. CAG:488

Ruminococcus sp. CAG:177

Clostridium sp. CAG:413 Coprococcus sp. CAG:131 Coprococcus eutactus strain 2789STDY5608888 Eubacteriaceae bacterium CHKCI005 isolate CHKC5

Coprococcus eutactus strain 2789STDY5834963 Clostridium sp. CAG:352 Clostridium sp.Clostridium L2-50 Scfld_02_19 sp. CAG:264 Clostridium sp. CAG:964 Coprococcus sp. CAG:782 Anaeromassilibacillus sp. An172 An172_contig_1 Clostridium sp. CAG:127 Eubacterium sp. CAG:581 Clostridium sp. CAG:590 Eubacterium sp. CAG:202

Ruminococcus bromii strain L2-36 contig000003

Lachnospiraceae bacterium NE2001 Ruminococcaceae bacterium P7 Ruminococcus bromii strain YE282

Lachnospiraceae bacterium strain LC2019 Ruminococcus sp. CAG:108

Ruminiclostridium sp. KB18 chromosome Eubacterium ruminantiumButyrivibrio strain ATCC crossotus 17233 CAG:259 Eubacterium ruminantium strain HUN269 Clostridium sp. CAG:1013

Clostridium sp. CAG:557 Anaerostipes sp. 992a contig000001 Clostridium sp. CAG:632 Anaeromassilibacillus sp. An250 An250_contig_1

Eubacterium sp. CAG:76 Anaeromassilibacillus sp. An200 An200_contig_1

Eubacterium sp. CAG:248 Clostridium sp. MSTE9 ctg120006483004 Eubacterium sp. CAG:86 Ruminococcaceae bacterium CPB6

Eubacterium sp. CAG:38 Clostridium sp. W14A NODE_1 Clostridium leptum CAG:27

Clostridium leptum DSM 753 Scfld_02_20

[Clostridium] leptum DSM 753 10c

Eubacterium eligens CAG:72 Clostridium methylpentosum DSM 5476 Scfld365

Lachnotalea glycerini strain DLD10 NODE_1000_LENGTH_1077_COV_0.824211_ID_1999 Anaerotruncus sp. G3(2012) Eubacterium sp. CAG:252 Lachnospira pectinoschiza strain 2789STDY5834836 Hydrogenoanaerobacterium saccharovorans strain CGMCC 1.5070 [Eubacterium] eligens ATCC 27750 chromosome Clostridium sp. CAG:169

Lachnospira multipara strain D15d Clostridium sp. CAG:242 [Eubacterium] eligens strain 2789STDY5834878 Clostridium sp. ATCC 29733 Butyrivibrio sp. CAG:318 Lachnospira pectinoschiza strain M83 Clostridium sp. DSM 4029

Anaerotruncus colihominis strain An25

Anaerotruncus colihominis DSM 17241 Scfld_02_27

Acetanaerobacterium elongatum strain CGMCC 1.5012 [Bacteroides] pectinophilus ATCC 43243 Scfld_02_8 [Clostridium] fimetarium strain DSM 9179 Ruminococcaceae bacterium D5

Ethanoligenens harbinense YUAN-3 Lachnospiraceae bacterium XBB1006 [Clostridium] cellulosi Clostridiales bacterium CHKCI001 isolate CHKC1 Euba Robinsoniella sp. RHS robin_c1 Eubacteriumcterium sp. CAG:786 sp. CAG:115 1 An251_contig_1 Eubacterium siraeum CAG:80 Anaerocolumna aminovalerica strain DSM 1283 Anaerocolumna jejuensis DSM 15929 [Eubacterium] siraeum strain 2789STDY5834928

Eubacterium siraeum 70/3 draft Roseburia sp. CAG:303 Anaerocolumna xylanovorans DSM 12503 Acetivibrio ethanolgignens strain ACET-33324 ACET-33324.Scaf1 Ruminococcus albus 8 contig00071 Eubacterium sp. CAG:603 Ruminococcus albus SY3 scaffold00001

Anaerobium acetethylicum strain GluBS11 Ruminococcus sp. CAG:57 Clostridium sp. CAG:411 [Clostridium] polysaccharolyticum strain DSM 1801 Ruminococcus bicirculans chromosome I Lachnospiraceae bacterium RM5Herbinix sp. SD1D Ruminococcaceae bacterium FB2012 Herbinix hemicellulosilytica Ruminococcus sp. CAG:579

Ruminococcus sp. YE78

Ruminococcus sp.

Ruminococcus sp. CAG:353

Ruminococcus champanellensis type strain 18P13T draft

Ruminococcus sp. CAG:379 Anaerosporobacter mobilis DSM 15930 R uminococcus sp. CAG:624 Coprococcus sp. HPP0074 Rumi YE71 Eubacterium uniforme[Clostridium] strain ATCC populeti 35992 strain 743A Rumi Lachnoclostridium phytofermentans ISDg chromosome nococcus flavefaciens 0 Ruminococcus sp. 37_24 Ley3_66761_scaffold_0 Lachnoclostridium sp. An196 An196_contig_1Clostridium nexile CAG:348 nococcus fla Ruminococcus sp. CAG:254

Ruminococcus callidus Lachnospiraceae bacterium 6_1_37FAA Ruminococcus sp. CAG:403

Clostridium nexile DSM 1787 Scfld22 Ruminococcus sp. CAG:330 ve faciens strain YL228 Coprococcus comes CAG:19 Eubacterium sp. CAG:274

Lachnospiraceae bacterium 1_1_57FAA Tyzzerella sp. An114 An114_contig_1 0 7c Rf007c_contig00004 Lachnospiraceae bacterium 3_1_46FAA Clostridium sp. ASF356 [Clostridium] lactatifermentans DSM 14214

Anaerotignum lactatifermentans strain An75 An75_contig_1 ATC

Clostridium sp. CAG:505 C 27 Anaerotignum neopropionicum strain DSM-3847 CLNEO_contig000001 Coprococcus comes strain 2789STDY5834913Dorea formicigenerans CAG:28 760 Dorea formicigenerans 4_6_53AFAA [Clostridium] propionicum DSM 1682 Dorea longicatena CAG:42 Coprococcus comes strain 2789STDY5834866 [Clostridium] propionicum DSM 1682

Clostridium lentocellum DSM 5427 Dorea sp. CAG:105 Dorea sp. D27 Epulopiscium sp. Nele67-Bin005 Nele67M_MBin0021

Epulopiscium sp. SCG-B05WGA-EpuloA1 SCGB05WGA_1

Dorea sp. 5-2 Epulopiscium sp. SCG-B11WGA-EpuloA1 SCGB11WGA_1 Dorea longicatena strain 2789STDY5608866 Dorea sp. CAG:317 Epulopiscium sp. SCG-D08WGA-EpuloA1 SCGD08WGA_1

Epulopiscium sp. AS2M-Bin002 AS2M_MBin02_1 Dorea longicatena strain 2789STDY5834914 Epulopiscium sp. AS2M-Bin001 AS2M_MBin01_1 Lachnospiraceae bacterium 5_1_57FAA Epulopiscium sp. Nuni2H_MBin003 Nuni2HMBin003_1 Clostridium hylemonae DSM 15053 Clostridium scindens ATCC 35704 Scfld_02_40 Epulopiscium sp. SCG-C07WGA-EpuloA2 SCGC07WGA_1 Dorea formicigenerans ATCC 27755 D_formicigenerans-3.0.1_Cont400 Epulopiscium sp. Nele67-Bin004 Nele67MMBin003_1

Epulopiscium sp. Nele67-Bin001 Nele67MMBin001_1 Lachnospiraceae bacterium 3-2 Epulopiscium sp. Nuni2H_MBin001 Nuni2HMBin001_1

Epulopiscium sp. Nele67-Bin002 Nele6n7_1018

Coprococcus catus GD/7 draft

Johnsonella ignava ATCC 51276

Clostridiales bacterium KLE1615

RuminococcusRuminococcus gnavus CC55_001C gnavus CAG:126 Eubacterium cellulosolvens 6 chromosome Lachnospiraceae bacterium TWA4 TWA4_contig00290 Lachnoclostridium sp. An118 An118_contig_1 Ruminococcus torques CAG:61 Candidatus_Lachnoanaerobaculum_GGB1_strain_JCVI_32_bin.65 Lachnoanaerobaculum saburreum F0468 ctg120007834031

Lachnospiraceae oral taxon 107 str. F0167

Lachnospiraceae bacterium 8_1_57FAA Ruminococcus sp. CAG:55 Lachnoanaerobaculum sp. ICM7 ctg120007550942

[Ruminococcus] gnavus strain RJX1121 RJX1121_1 Ruminococcus torques L2-14 draft Lachnoanaerobaculum sp. OBRC5-5 Lachnoanaerobaculum sp. MSX33 contig00033

Lachnoanaerobaculum saburreum strain DNF00896 Lachnoclostridium sp. An76 An76_contig_1 Lachnospiraceae bacterium oral taxon 082 str. F0431 Lachnospiraceae bacterium ACC2 Ruminococcus lactaris CC59_002D Clostridium sp. D5 Catonella morbi ATCC 51271

Candidatus_Lachnospiraceae_FGB1_strain_JCVI_47_bin.6

Candidatus_Lachnospiraceae_FGB1_strain_JCVI_44_bin.29 Clostridium sp. C105KSO13 [Clostridium] aminophilum strain F

[Clostridium] aminophilum strain KH1P1

[Ruminococcus] torques strain 2789STDY5608867 Lachnospiraceae bacterium CAG:215 Clostridium sp. ASF502 Oribacterium sp. KHPX15 Oribacterium sp. WCC10

Lachnospiraceae bacterium JC7 contig00001

Oribacterium sp. C9 NODE_10_length_131389_cov_687.311_ID_8143 Lachnoclostridium sp. An298 An298_contig_1 Ruminococcus lactaris ATCC 29176 Scfld_02_46 Oribacterium sp. oral taxon 078 str. F0263 Oribacterium sp. oral taxon 078 str. F0262

Lachnospiraceae bacterium M18-1 Candidatus_Lachnospiraceae_FGB1_strain_JCVI_3_bin.3 Lachnoclostridium sp. An169 An169_contig_1 Oribacterium sinus F0268 Oribacterium sp. oral taxon 108 str. F0425 noncontiguous_finished_chromosome

Blautia sp. KLE 1732 Oribacteriumsp. ACB1 Blautia sp. SF-50 Oribacterium parvum ACB8 ctg120007730861 Coprococcus sp. HPP0048 Clostridium hathewayi CAG:224 Hungatella hathewayi strain 2789STDY5608850

Clostridium sp. CAG:58 Drancourtella sp. An177 An177_contig_1 Clostridium sp. CAG:81 Clostridiales sp. SS3/4 draft [Eubacterium] contortum strain 2789STDY5834876 Drancourtella sp. An210 An210_contig_1 Ruminococcus sp. CAG:17 Clostridium sp. CAG:7 Clostridiales bacterium 1_7_47_FAA supercont2.108 Drancourtella sp. An57 An57_contig_1 Ruminococcus sp. CAG:90 Clostridium hathewayi WAL-18680 Hespellia stercorisuis DSM 15480 [Clostridium] lavalense strain NLAE-zl-G277 Drancourtella sp. An12 An12_contig_1 Blautia sp. CAG:237 Clostridium asparagiforme DSM 15981 Clostridium sp. FS41 CLFS41_contig000001 Blautia sp. CAG:257 Clostridium citroniae WAL-17108 [Clostridium] citroniae strain NLAE-zl-G70 Ruminococcus sp. DSM 100440 contig00001 [Clostridium] clostridioforme strain ATCC 25537 [Clostridium] bolteae strain ATCC BAA-613 chromosome Lachnoclostridium sp. YL32 Ruminococcus sp. SR1/5 draft Clostridium clostridioforme CAG:511 Clostridium bolteae 90A5 Clostridium bolteae CAG:59

Clostridium clostridioforme CAG:132

Clostridium sp. C105KSO14

[Clostridium] clostridioforme WAL-7855

Lachnoclostridiumsp. An14 An14_contig_1 Clostridium sp. chh4-2 Scaffold1

[Clostridium] celerecrescens strain 152B c1 [Desulfotomaculum] guttoideum strain DSM 4024

Ruminococcus obeum CAG:39 [Clostridium] celerecrescens 18A H171DRAFT_unitig_0_quiver.1

Clostridium sp. C105KSO15 Clostridium sp. ASBs410 K413DRAFT_scaffold00001.1_C [Clostridium] saccharolyticum WM1 chromosome

[Clostridium] sphenoides JCM 1415 strain ATCC 19403

Clostridiales sp. SM4/1 draft

Ruminococcus sp. CAG:9

Blautia sp. CAG:37

Blautia obeum strain 2789STDY5608837 Ruminococcus obeum A2-162 draft

Ruminococcus sp. CAG:60

Blautia sp. CAG:52

Blautia wexlerae strain 2789STDY5834911 Blautia sp. An249 An249_contig_1 Blautia hansenii DSM 20583 Blautia hydrogenotrophica CAG:147

Blautia hydrogenotrophica DSM 10507 Blautia wexlerae strain 2789STDY5834863 Roseburia sp. CAG:471 Blautia sp. An46 An46_contig_1

Clostridium sp. M62/1

Blautia sp. YL58 chromosome Blautia coccoides strain YL58

Clostridium sp. CAG:43

Clostridium sp. CAG:149

Clostridium sp. CAG:299

Blautia sp. An81 An81_contig_1

Clostridium sp. 7_3_54FAA

Lachnospiraceae bacterium CAG:364 Blautia coccoides strain NCTC11035

Ruminococcus sp. 5_1_39BFAA acpfZ-supercont2.3

Lachnospiraceae bacterium 10-1 Clostridium sp. HMb25 unitig_0

Blautia hydrogenotrophica strain 2789STDY5608857

Blautia hansenii DSM 20583 chromosome

Lactonifactor longoviformis DSM 17459

Clostridium symbiosum WAL-14673

Clostridium symbiosum WAL-14163

Marvinbryantia formatexigens strain I-52

Lachnoclostridium sp. An131 An131_contig_1

Clostridium saccharolyticum-like K10 draft Lachnoclostridium sp. An138 An138_contig_1

Parasporobacterium paucivorans DSM 15970

Fusicatenibacter saccharivorans strain 2789STDY5834885

Fusicatenibacter saccharivorans strain 2789STDY5834923

Marvinbryantia formatexigens DSM 14469 B_formatexigens-1.0.1_Cont57.1 Supplemental Fig. S2: Phylogenetic placement of unknown species-level genome bins

(uSGBs) within Bacteroidales, Clostridiales, and Saccharibacteria. Bacteroidales and

Clostridiales trees were generated using PhyloPhlAn2 (Pasolli et al. 2019) and the

Saccharibacteria tree was generated using Anvi’o. All trees were visualized using iToL (Letunic and Bork 2019). (A) Bacteroidales (B) Clostridiales and (C) Saccharibacteria

Figure S3 A

Candidatus_Saccharibacteria_TM7_EAM_G5_2_HOT_356strain_TM7_EAM_G5_2_HOT_356

Candidatus_Nanosyncoccus_FGB4_strain_JCVI_47_bin_30

Candidatus_Nanosyncoccus_FGB2_strain_JCVI_32_bin_36

Candidatus_Nanosyncoccus_FGB3_strain_JCVI_44_bin_1

Candidatus_Saccharibacteria_TM7_KMM_G3_1_HOT_351strain_TM7_KMM_G3_1_HOT_351

Candidatus_Nanosyncoccus_FGB1_strain_JCVI_1_bin_4

Candidatus_Nanosyncoccus_GGB1_strain_JCVI_5_bin_8

Candidatus_Saccharibacteria_TM7_CMJM_G6_1_HOT_870strain_TM7_CMJM_G6_1_HOT_870

Candidatus_Nanogingivalaceae_FGB1_strain_JCVI_32_bin_33

Candidatus_Saccharimonas_sp__strain_JCVI_32_bin_49

Candidatus_Nanogingivalaceae_FGB1_strain_JCVI_28_bin_11

Candidatus_Nanogingivalaceae_FGB1_strain_JCVI_27_bin_3

Candidatus_Nanogingivalaceae_FGB1_strain__JCVI_1_bin_12

candidate_division_TM7_single_cell_isolate_TM7c

Candidatus_Nanosynbacter_GGB4_strain_JCVI_6_bin_3

Candidatus_Nanosynbacter_TM7c_strain_JCVI_1_bin_5

Candidatus_Nanosynbacter_TM7c_strain_JCVI_32_bin_19

Candidatus_Nanosynbacteraceae_FGB1_strain_JCVI_32_bin_22

Candidatus_Nanosynbacter_UMGS1926_strain_JCVI_1_bin_14

TM7_phylum_sp_oral_taxon_952strain_TM7x

Candidatus_Nanosynbacter_GGB1_strain_JCVI_3_bin_14

Candidatus_Nanosynbacter_GGB3_strain_JCVI_36_bin_4

Candidatus_Nanosynbacter_TM7c_strain_JCVI_6_bin_10

Candidatus_Saccharimonas_aalborgensisTM71

Candidatus_Nanosynbacteraceae_FGB2_strain_JCVI_32_bin_44

Candidatus_Nanosynbacter_GGB2_strain_JCVI_32_bin_57

Candidatus_Nanosynbacter_sp__TM7_MAG_III_A_2_strain_JCVI_32_bin_12

Candidatus_Nanosynbacter_sp__TM7_MAG_III_A_2_strain_JCVI_6_bin_12 . . . . . r s y. in e yr .1 .II. .III ter ter yX uA xin xin a mB r r ase unit unit unit ase ase unit ase ase unit ase ase unit ase unit unit e n r as e iant. r ases b b b b b amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily amily ylase amily ..p T .UbiE utase unit.a yth r e r e r e r e r e r .MutL .SufC .CorA f f f f f f f f .T h f amily. amily. . T r .CwlO .CopZ .SpoU a r r xylase .RecQ f . f f .CobQ .ligase amily.I .YwqE .MoaA ulence e r mation f .. f .kinase .kinase .kinase .kinase .kinase .kinase etolase e e m .protein .activity .protein .protein e .clas s e e .antigen .domain .activity. .activity. te r e k ydrolase ydrolase .channel .enzyme A5.YrdC minators o r e ..clas s .aldolase r .domains .domains .domains e as e as e .S.cluster r .path w anspo unit.SecE .synthase .synthase h e .su b ans f ans f ans f ans f ans f . f .ErfK.SrfK as e ucleas at e e .reductase .reductase .reductase .reductase adR. f e ylas e v e xin.module ansposase xin.module ans f .isome r as e ylas e e an e ..pTh r ucleotidase ylas e .synthetase .thiored o ac e r PKD.repeat .deaminase r as e e e e ydrogenase .component ydrogenase ydrogenase .component ydrogenase .component ylat e r xypeptidase T P T P .super f .super f .synthetas e .CoA.kinase ..G3E. ..IscR. e an e .desulfu r Glycosidase .YbaK.EbsC ated. v Rubre . F u v h ..LCP.. f Glutared o as e as e T e as e ylt r ug.activity.B. ylt r ylt r ylt r r e .components h e r ansacetylase ..MarR. f .. P minal.su minal.su e o .super f e ating.enzyme ating.enzyme an e ..beta.su b e ..SIS..domain ..GH57. f ..GH16. f idylat e s .antirepressor amily.enzyme Malic.enzyme r .su b r asin.domain r . A ly.protein.PilN .alpha.su n .o r ...GH15. f .alanin .CBS.domains v r e ed.in.vi r ydrolas ..alpha.su b ..NUDIX. f Acetat e e e itin.li k ..HSP90. f v . f e .enzym e e .decarb o anspo ed.protein.YjaZ olat e as e e .synthas e .d r .cyclo h s T P ly. A T P ibo n Sur f as e s h Py r .related.enzyme U r old.protein.SufB e ..DUF218. f .de h .de h s ed.protein.YqeY idylylt r e ..epsilon.su O.antigen.ligase .acid.t r anching.enzyme anching.enzyme .III..delta.su as e .pSe r .aldolas ymidylat e ..gamma.su b ed.in.DNA.repair Predicted.kinase Endo n A i z .domain.o Shikimat e as e F r r iptional.regulato v Phospho ans f ..DUF1287. f .AlkP.super f Gua n .chaperon ol v .anchored.protein .AP.l y er r s as e e .o f r .regulation.protein r T P .carb o ..MPP.super f .related.deacylase .met h .resistanc e v ..AAA..super f meas e meas e minal.PDZ.domain .C.met h .acti v minal.HTH.domain xy r e .u r .associated.protein ymidylat e Ca2..Na..antipo yl.tRNA.synthetase Glycogen.synthase T h e T P .S.cluste r r .inacti v ij F A ..C.te r ..N.te r e e s ol v e s .phosphodieste n atD..DNas e ..PNPOx.li k .o f xin.antit o ..MmcQ.YjbR. f xin.antit o ..MazG..super f xymet h .AMPylation.domain e as e .isome r e acid.de ylt r xin.NADP.reductase olat e ydro f GT P .system.kille r e v as e amat e ajQ..UPF0234. f r y..VirB6.components .o r r Y T e acil.DNA.glycosylase ac e ..PP.loo p e ..queuin ysM.i n iphosphat .Cystein e al.memb r e T T h ..memb r unit.TsaC.S U Y acte r a .polypre as e ..UTP.ammonia.l y .it s as e .t o .t o .assem b x y Glucan.phospho ..colanic..teichoic.acid. Ribosomal.protein.L34 .2..O..met u r Amin o iphosphat r amily. A ansc r .YbiA..DUF1768. f t.chain.de h r .i n ..CofD.UPF0052. f ly.scaf f .bisphosphat unit.. f ..pe r Phosphomanno .dependent.te .alpha.beta.super yrophosphat .lactat e .protein..Rec F anspeptidas Phosphot U r Prophag .t r Dephosph as e Di h s ich.repeat..LRR..protein anslocas r .assem b amily.phospho ydr o e ydrolase o .l y .reductas e .isome r adical.acti Coppe .t r .t r as e e ylglucosamin f T P yldiphosphat ydrorhamnos ymidylat e as e .isome r r yrophosphat . r as e ydro f .G A ection.protein..PIP.. f h .and. A e e o TP.synthas e ylas e .su b .chaperon . h xidas e e as e p oat e e unit..helicas as e .synthetas e etolas e etolas e yl. p ydrolas r erred o ydr o .th e v tRNA.G46.met h al.moti f .mechanosensiti TP.synthas e Methio n ed.conse r .II..o ed.protein..UPF0160. ed.in. F ytR.Cps2A.Ps r amily..contain .l y ydroorotat e T h .protein.phosphatas T P Sho r .pilu s a h amily.II.DNA.helicas . A acto r Predicted.met h h ibos e n ed.sur f .biosynthesi F . o .chaperonin.GroES..HSP10. u v ed.phag e r e ..all.alpha.NTP.P P ing.t r Predicted.memb .in f ..integ r L yl.dieste r . f e TP.synthas e iptional.regulato i z i z . A .antibiotic .th e ..modulato r t.system.. . f Beta.glucanas in e TP.synthas e Uncha r r .o f mat e .protein.YjjP..DUF1212. X5..3...de o i z e e y.path w .MazE F .MazE F iptional.regulato iptional.regulato p i z r yl.D.alanin .protein.HdeD..DUF308. .protein.YhhQ..DUF165. f ..MoaA.NifB.PqqE.SkfB. f Malat e s ol v y r e ... .Zn2..upta k .bisphosphat . A e anin.domain.containing.protein Di h Tf p .peptidoglycan. C o . A .protein.YbhN..UPF0104. .contain. L .glycogen.deb e v ans k ans k p o r t.system..pe r .assem b ed.protein. f .biosynthesi .1.phosphat Mg2..and.Co2..t r uctu r ibosyl as e r r meas e .tagatos e .beta.su b r .isome r .Zn.Cd.efflux.system.component e n Glycyl.tRNA.synthetas e ans f ed.protein. . f .RsmH.met h e r .se r acto r .with.duplicated. .clas s ucleosid Leucin i z yl.tet r T T an e .S.cluste r .th e .th e ucleotid DNA.polyme xyben z v .alpha.mannosidas an e an e ..M r Organic. r acte r acte r .maintenanc f f e r TP.synthas e Chaperonin.GroEL..HSP60. ansc r .G5.and.tandem.DUF348.domains HD.super Super f r r .and.PhoH. f e xycytidin e r acte r r xA..RecA.mediated.autopeptidas n .CAP..CSP.antigen.5.PR1..domain an e Isopente n yrosin e acte r ..E3..component.o r r C o e .o f .DNA.glycosylas DNA.mismatch.repai ansc r ansc r r s uABC..Zn.binding.component.Z .desucci n r Molecula at e r s F T as e .RimI.and.related.acetylt Diacylglycerol.kinas anspo r r . A .responsi e2..o r e CTP.synthas e Predicted. A Preprotein.t r y.contain.an.N.te r e ylcystein e D.ala n as e oF1.typ e ter s n e r dTDP.4.de h X1.4.alpha.glucan.b e uctos e r ibo n yrophospho as e F v r .synthetas e o ..BPG.independent..AlkP.super .a.related.enzym oF1.typ e .L e ydr o ..som e amily..contain.C.te ydrolas F e r UDP.N.acetyl m .related.2. h ...alpha.su b r u v acte r ..protein.threonin .associated.phospholipid.phosphatase ans f r anspo ly..pe r p .secreto r De o e Thiol.disulfid r uctos e mination.at.Rh .enzym e Predicted. A .related.t o ylas e Undecapre F .related.protein..contain TP.binding.protein.i r Plastoc y .and.phosphosuga Ribo oF1.typ e F r .reductas e um.co f ibosylt r r oF1.typ e . V s T P tRNA.G18.. r

Glycin e Gene Copy Number r .wing.st r .DNA.polyme .o r .h a F ..prolyl.tRNA.editing.enzym .DNA..protein.cystein .S.cluste r e m n mation...metallophosphatas .I V F r F Uncha Uncha e .Methe n A Py r .5..phosphat e e Phospho Uncha .protein.YcgQ...UPF0703.DUF1980. ..all.alpha.NTP.P P an e .RNas e e e ans f Glycopeptid Uncha l e .protein.DedA..SNARE.associated.domain X4. h Fid o e as e Selenocystein .reductas e Pullulanas as e o r e utas e Reference genome F ed.memb r b ed.conse anspo Prophag amily.enzym ed.memb r e as e . f .activity.HflC..stomatin.prohibitin.super f yrophosphatas ..glucan.1.4.alpha.glucosidas e r yp e UTP.glucos e oF1.typ e ed.memb r e r i z ed.SAM.binding.protein.Ycd i z ed.in.LPS.biosynthesi e Uncha i z . m an e T Glycerophospho .menaquinon an e amily..m a e r Small.conductanc F .with.duplicated.suga . p .and.related.RCC1.domain.containing.proteins y.als o .system.Z i z .O.acylt r i z ydrogenas Predicted.phospho .MdoB.o r minal.domain.o r .assem b ed.in.lipoprotein.releas e Lipoprotein.ancho NifU.homolog.i s e y.protein s ucleas e abE..contain .and.inhibito ol v r Alpha.a r ans f at e .Mn2..Zn2..t ial.gluconeogenesi Anaerobic. xamin e DNA.binding.t Memb r ..S1.C.sub f ans f Y UDP.N.acetylenol v ibosylt r Predicted. h Molybde r yladenosin .protein.YhgE..phag id e ylas e titioning. ol v DNA.binding.t DNA.binding.t acte r acte r ans f as e ylguanin r Predicted. A acte r xin.component.o xin.component.o r o 6 .ABC.t r v r r .de h .Mn2..Zn2..t r xo n ed.in.anti.te r acte r .i n acte r o ucleotid Recombinational.DNA.repai id o .biosynthesi ..deacylas e Hemolysin.o n r .NYN.typ e e ydrogenas e r r r n ydrogenas .cleaning.NTP. an e .o f .proteas e ..t .. e .pa r y r yl.diaminopimelat ol v s e e ed.N.te r iptional.represso e khead.associated..FHA..domain..bind as e v ed.memb r .o f .Bacte r ed.memb r .S.cluste r Antit o ans f i z Phosphopantothen .de h r .tRNA. r .NADPH.quinon .amidot r .Zn.upta k e r o r iphosphat .amidot r Ubiquinon r Uncha i z .de h e Uncha Ribo i z Uncha e e yrophosphatas ..i n ABC.typ e .proteas e F Glucoa m Uncha O6.met h Uncha p .t r s as e ed.PurR.regulated.memb ed.protein. ylcarbam .NBD.HSP70. f e ansc r ABC.typ e v ed.protein.YkwD..contain i z in e ans f ucleas ulin.suppresso .Succi n acte r e r r v r .tRNA.Pr o olat e t.system..i r .polysaccha acte r .t r n Nucleotidylt all.polyme acte r e r r r xoDNAs e .t r ed.memb r r .shock.protein.PspC..stres s Radical.SAM.super Phosphoglyce Lactat e .th e ed.in. F w iptional.regulato Putati v i z ydrolipoamid Regulato ans f ac e Cy s .component ed.protein.. p acte r .o f ABC.typ e

..contain s 4 r Glutamin e ol v ydro f .YlaK..contain s Chromosom .t r i z v e lB.and.related.protein Uncha ycoplasm Ribosomal.protein.S18.acetylas .and.related.regulato Suga r anspo .RsmA.KsgA.DIM1..m a a h Uncha as e Uncha Sur f Phag e acte r ansc r e x..di h at.protein.secretion.system.quality.control.protein. .xanthosin r r ed.conse Alpha.tu b .t r .F r T .and.related.hous ed.conse i z T P .protein.CapA.YwtB..capsul acte r as e iplasmic.se .tet r i z Uncha .kinas e r ading.endo A s .deacetylas r ucleas e r Phosphoglycerol.t e r e .and. m Anionic.cell. P .L.lactat e tRNA.A37.threo n SOS.respons e Uncha .Mut T acte r Inosin e o .compl e r .synthetas e acte r

e This study: healthy S.adenosylmethionin ylen e t.system.i n TP.dependent. e ibo n ans f r e Suga r e r HD.GYP.domain..c.di.GMP.phosphodieste Predicted.NAD.dependent.protein.ADP. Uncha A ABC.typ e nithin ylt r

Predicted.DNA.binding.protein.with.dou 2 h micute s ansglycosylas Uncha mRNA.deg .biosynthesi Uncha anspo .6.P.deglycas e e e .cleaning.noncanonical.NTP. .t r aZ..DNA.binding.t Acetylo r e .in.Fi r ydrogenas Predicted. r X5.10.met h M r .6.phosphat urein.t r e as e yrophosphatas v .de h p Archaeal.2.phosph at e ABC.typ e r .lytic. m

uctoselysin 0 l e F r .dGTP. x o Predicted.hous Glucosamin xogluta Solu b oly.gamma.glutamat X8. o P y.junction.resol .2. o a This study: caries at e u v Py r X16S.rRNA.A1518.and.A1519.N6.dimet old.protein..predicted.Hollid .H. f RNas e B Key G1 G3 Cell Wall Purine Metabolism Metabolism cyan yellow blue murC/D Pyrimidine Thiamine black Metabolism Metabolism green red Dolichyl orange Metabolism

G6 Rhamnose 1 Carbon Metabolism Metabolism

Glycolysis/ Glycerophospholipid Heme Central Carbon Metabolism Metabolism Metabolism Anthranilate CoA-Ligase

Ubiquinone Metabolism Lactate Dehydrogenase

TCA Cycle Arginine Metabolism

Other Sugar Metabolism

Selenocysteine Lyase

F1F0 ATPase F1F0 ATPase Supplemental Fig. S3: Fucntional pathways encoded by oral Saccharibacteria clades G1,

G3, and G6. (A) Differences in encoded COG functions pathways across human- associated Saccharibacteria. Heatmap illustrating the presence of various genes across 4 major clades of human-associated Saccharibacteria. Rows and columns were clustered using the Jaccard distance and the “complete” clustering method. Only COG functions that were significantly different between clades are shown (adjusted q-value < 0.05). (B) Metabolic circuit indicating the metabolic pathways encoded by Saccharibacteria clades G1, G3, and G6.

KEGG KO pathways present in the Saccharibacteria clades, using the TM7x,

TM7_KMM_G3_HOT351, and TM7_G6_1_HOT870 genomes as representatives.

Figure S4

A Taxonomic abundance Bar graphs (relative abundance) Caries Healthy

'Corynebacterium durum' 'Atopobium parvulum' 'Atopobium rimae' 'Olsenella uli' Slackia 'Cryptobacterium curtum' 'Leptotrichia buccalis' 'Leptotrichia wadei' 'Leptotrichia hofstadii' 'Leptotrichia shahii' 'Leptotrichia goodfellowii' 'Leptotrichia sp. oral taxon 215' 'Fusobacterium nucleatum' Tree Branches (taxa of interest) 'Fusobacterium necrophorum' 'Fusobacterium periodonticum' 'Treponema denticola' 'Treponema maltophilum' 'Rothia aeria' 'Treponema lecithinolyticum' S. mutans and S. sobrinus 'Treponema socranskii' 'Treponema medium' 'Treponema vincentii'

'Ca. Nanosynbacter TM7b' 'Cutibacterium acnes' 'Rothia mucilaginosa' 'Rothia dentocariosa' 'Scardovia wiggsiae' Prevotella 'Ca. Nanosynbacter TM7c' 'Schaalia georgiae' 'Mycoplasma orale' 'Fretibacterium fastidiosum' 'Alloscardovia omnicolens' 'Bifidobacterium longum' 'Schaalia odontolytica'

'Bifidobacterium dentium' Rothia 'Streptococcus phage Dp-1' 'Corynebacterium matruchotii' 'Parascardovia denticolens' 'Lactobacillus phage Lc-Nu' 'Actinomyces sp. ICM58' 'Actinomyces sp. ICM39' 'Actinomyces sp. HPA0247' Ceduovirus 'Actinomyces sp. ICM47' 'Actinomyces oris' Haemophilus 'Propionibacterium phage PAS50' 'Actinomyces johnsonii' 'Streptococcus phage Cp-1' Riemerella

'Pseudopropionibacterium propionicum' 'Streptococcus phage EJ-1' Neisseria 'Actinomyces sp. oral taxon 448' 'Actinomyces'Actinomyces massiliensis' viscosus' 'Human betaherpesvirus 7' 'Actinomyces sp. oral taxon'Actinomyces 172' graevenitzii' 'Human betaherpesvirus 6B' 'Actinomyces naeslundii' Viruses 'Human gammaherpesvirus 4' 'Bacteroidetes oral taxon 274' 'Torque teno virus' 'Capnocytophaga granulosa' 'Torque teno virus 12' 'Capnocytophaga ochracea' 'Bacteroides'Tannerella pyogenes' forsythia' 'Murine osteosarcoma virus' 'Capnocytophaga gingivalis'

700500300100

'Porphyromonas catoniae'

'Porphyromonas sp. oral'Alloprevotella taxon 279' rava' 'Porphyromonas'Porphyromonas endodontalis' gingivalis' 'Alloprevotella tannerae'

'Prevotella'Prevotella sp.'Prevotella oral saccharolytica' taxon sp. 306' C561' 'Streptococcus gordonii' 'Prevotella histicola' 'Streptococcus salivarius' 'Prevotella maculosa' 'Streptococcus sanguinis' 'Prevotella nanceiensis' 'Prevotella pleuritidis' 'Streptococcus thermophilus' 'Prevotella conceptionensis' 'Streptococcus mutans' 'Prevotella multiformis' 'Streptococcus sobrinus' 'Prevotella salivae' 'Prevotella micans' 'Streptococcus agalactiae' 'Prevotella marshii' 'Streptococcus pyogenes' 'Prevotella pallens' 'Streptococcus parasanguinis' 'Prevotella veroralis' 'Streptococcus anginosus' 'Prevotella oulorum' 'Streptococcus intermedius' 'Prevotella oris' 'Prevotella oralis' 'Streptococcus vestibularis' 'Prevotella nigrescens' 'Streptococcus mitis' 'Prevotella melaninogenica' 'Streptococcus cristatus' 'Prevotella intermedia' 'Streptococcus peroris' 'Prevotella denticola' 'Streptococcus infantis' 'Prevotella buccae' 'Prevotella loescheii' 'Streptococcus constellatus' 'Enhydrobacter aerosaccus' 'Streptococcus australis' 'Campylobacter gracilis' 'Streptococcus pseudopneumoniae' 'Campylobacter showae' 'Campylobacter rectus' 'Streptococcus sp. M334' 'Campylobacter concisus' 'Streptococcus oralis subsp. tigurinus' 'Cardiobacterium hominis' 'Streptococcus sp. SK140' 'Escherichia coli' 'Lactobacillus gasseri' 'Pseudomonas stutzeri' 'Moraxella catarrhalis' 'Lactobacillus fermentum' 'Aggregatibacter actinomycetemcomitans' 'Lactobacillus rhamnosus' 'Acinetobacter junii' 'Aggregatibacter'Aggregatibacter aphrophilus' segnis' 'Granulicatella adiacens' Actinobacillus 'Granulicatella elegans' 'Haemophilus paraphrohaemolyticus' 'Abiotrophia defectiva' 'Haemophilus sputorum' 'Haemophilus'Haemophilus parahaemolyticus' pittmaniae' 'Gemella haemolysans' 'Haemophilus parainfluenzae' 'Gemella morbillorum'

'Gemella sanguinis' 'Haemophilus'Haemophilus haemolyticus' influenzae' 'Gemella bergeri' 'Staphylococcus hominis' 'Oribacterium parvum ACB1' 'Acidovorax ebreus' 'Oribacterium parvum ACB8' 'Lautropia mirabilis' 'Oribacterium sinus' 'Eikenella'Ralstonia corrodens' pickettii' 'Neisseria sp. oral taxon 014' 'Oribacterium sp. oral taxon 078' 'Simonsiella muelleri' Thiomonas 'Lachnoanaerobaculum saburreum' 'Kingella denitrificans' 'Lachnoanaerobaculum sp. ICM7' 'Neisseria bacilliformis' 'Kingella oralis' 'Johnsonella ignava' 'Kingella kingae' 'Parvimonas sp. oral taxon 110' 'Neisseria polysaccharea' 'Catonella morbi' 'Neisseria subflava' 'Neisseria macacae' 'Neisseria meningitidis' 'Shuttleworthia satelles' 'Neisseria elongata' 'Neisseria gonorrhoeae' 'Lachnospiraceae bacterium oral taxon 082'

'Selenomonas artemidis' 'Neisseria lactamica' 'Lachnospiraceae bacterium oral taxon 500' 'Solobacterium moorei' 'Neisseria flavescens' 'Neisseria sicca'

'Centipeda periodontii' 'Stomatobaculum longum'

'Neisseria cinerea' ' yurii' 'Bulleidia extructa' 'Parvimonas micra' 'Peptoanaerobacter stomatis' 'Peptostreptococcus stomatis' 'Filifactor alocis' ' brachy' ' saphenum' Mitsuokella ' infirmum' Eubacteriaceae 'Veillonella parvula' 'Veillonella atypica' 'Veillonella dispar' 'Veillonella sp. 6 1 27' 'Veillonella sp. oral taxon 158' 'Veillonella sp. oral taxon 780' 'Veillonella sp. HPA0037' 'Anaeroglobus geminatus' 'Megasphaera micronuciformis' 'Dialister invisus' 'Selenomonas sputigena' 'Selenomonas flueggei' 'Selenomonas infelix'

'Selenomonas noxia'

B C Functional pathway Taxonomic abundance heatmap abundance heatmap Caries Healthy Caries Healthy

PWY−5100 pyruvate fermentation to acetate and lactate II Leptotrichia goodfellowii PWY−3001 superpathway of L−isoleucine biosynthesis I THRESYN−PWY superpathway of L−threonine biosynthesis Lachnospiraceae bacterium oral taxon 082 PWY−841 superpathway of purine nucleotides de novo biosynthesis I PWY−7228 superpathway of guanosine nucleotides de novo biosynthesis I Lachnoanaerobaculum saburreum PWY0−166 superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli) PWY−6125 superpathway of guanosine nucleotides de novo biosynthesis II Selenomonas artemidis PWY−6126 superpathway of adenosine nucleotides de novo biosynthesis II PWY−5097 L−lysine biosynthesis VI Selenomonas sputigena ARO−PWY chorismate biosynthesis I COMPLETE−ARO−PWY superpathway of aromatic amino acid biosynthesis PWY−6121 5−aminoimidazole ribonucleotide biosynthesis I Selenomonas infelix PWY−6122 5−aminoimidazole ribonucleotide biosynthesis II PWY−6277 superpathway of 5−aminoimidazole ribonucleotide biosynthesis Candidatus Prevotella conceptionensis PWY−7111 pyruvate fermentation to isobutanol (engineered) ILEUSYN−PWY L−isoleucine biosynthesis I (from threonine) Eubacterium yurii VALSYN−PWY L−valine biosynthesis PWY−724 superpathway of L−lysine, L−threonine and L−methionine biosynthesis II Aggregatibacter aphrophilus BRANCHED−CHAIN−AA−SYN−PWY superpathway of branched amino acid biosynthesis PWY−5103 L−isoleucine biosynthesis III Escherichia unclassified NONMEVIPP−PWY methylerythritol phosphate pathway I PWY−5973 cis−vaccenate biosynthesis PWY−7663 gondoate biosynthesis (anaerobic) Haemophilus paraphrohaemolyticus PWY−6609 adenine and adenosine salvage III COA−PWY coenzyme A biosynthesis I Actinobacillus unclassified PWY−7199 pyrimidine deoxyribonucleosides salvage PWY−4242 pantothenate and coenzyme A biosynthesis III Haemophilus sputorum PWY−6737 starch degradation V TRNA−CHARGING−PWY tRNA charging Neisseria subflava PWY0−1296 purine ribonucleosides degradation PWY0−1319 CDP−diacylglycerol biosynthesis II Prevotella saccharolytica PWY−5667 CDP−diacylglycerol biosynthesis I SER−GLYSYN−PWY superpathway of L−serine and glycine biosynthesis I PANTOSYN−PWY pantothenate and coenzyme A biosynthesis I Prevotella loescheii PANTO−PWY phosphopantothenate biosynthesis I PWY−6385 peptidoglycan biosynthesis III (mycobacteria) Neisseria macacae DTDPRHAMSYN−PWY dTDP−L−rhamnose biosynthesis I ASPASN−PWY superpathway of L−aspartate and L−asparagine biosynthesis Streptococcus oligofermentans PWY−7219 adenosine ribonucleotides de novo biosynthesis PWY−6147 6−hydroxymethyl−dihydropterin diphosphate biosynthesis I Aggregatibacter segnis PWY−1042 glycolysis IV (plant cytosol) PWY−2942 L−lysine biosynthesis III Leptotrichia buccalis COA−PWY−1 coenzyme A biosynthesis II (mammalian) PWY−6151 S−adenosyl−L−methionine cycle I PWY−6163 chorismate biosynthesis from 3−dehydroquinate Streptococcus peroris PWY−7221 guanosine ribonucleotides de novo biosynthesis PEPTIDOGLYCANSYN−PWY peptidoglycan biosynthesis I (meso−diaminopimelate containing) Capnocytophaga granulosa PWY−6386 UDP−N−acetylmuramoyl−pentapeptide biosynthesis II (lysine−containing) PWY−6387 UDP−N−acetylmuramoyl−pentapeptide biosynthesis I (meso−diaminopimelate containing) Cardiobacterium hominis PWY−6700 queuosine biosynthesis PWY−5686 UMP biosynthesis Actinomyces johnsonii PWY−7229 superpathway of adenosine nucleotides de novo biosynthesis I PWY−5695 urate biosynthesis/inosine 5'−phosphate degradation Lachnospiraceae oral taxon 107 PWY66−400 glycolysis VI (metazoan) GLYCOLYSIS glycolysis I (from glucose 6−phosphate) PWY−5484 glycolysis II (from fructose 6−phosphate) Leptotrichia hofstadii PWY0−162 superpathway of pyrimidine ribonucleotides de novo biosynthesis PWY−6168 flavin biosynthesis III (fungi) Aggregatibacter unclassified RIBOSYN2−PWY flavin biosynthesis I (bacteria and plants) PWY−7234 inosine−5'−phosphate biosynthesis III Oribacterium sp oral taxon 078 PWY66−422 D−galactose degradation V (Leloir pathway) PWY−6317 galactose degradation I (Leloir pathway) Corynebacterium durum ANAEROFRUCAT−PWY homolactic fermentation TRPSYN−PWY L−tryptophan biosynthesis Actinomyces massiliensis NONOXIPENT−PWY pentose phosphate pathway (non−oxidative branch) 1CMET2−PWY N10−formyl−tetrahydrofolate biosynthesis PWY−5347 superpathway of L−methionine biosynthesis (transsulfuration) Actinomyces naeslundii PWY−6936 seleno−amino acid biosynthesis PWY0−1061 superpathway of L−alanine biosynthesis Propionibacterium propionicum PWY−3841 folate transformations II HEMESYN2−PWY heme biosynthesis II (anaerobic) Actinomyces oris PWY−7197 pyrimidine deoxyribonucleotide phosphorylation PHOSLIPSYN−PWY superpathway of phospholipid biosynthesis I (bacteria) Eikenella corrodens PWY−5189 tetrapyrrole biosynthesis II (from glycine) PWY−5918 superpathay of heme biosynthesis from glutamate Campylobacter gracilis FASYN−INITIAL−PWY superpathway of fatty acid biosynthesis initiation (E. coli) PWY−7388 octanoyl−[acyl−carrier protein] biosynthesis (mitochondria, yeast) PWY0−862 (5Z)−dodec−5−enoate biosynthesis Porphyromonas endodontalis PWY−6282 palmitoleate biosynthesis I (from (5Z)−dodec−5−enoate) FASYN−ELONG−PWY fatty acid elongation −− saturated Treponema denticola PWY−7664 oleate biosynthesis IV (anaerobic) PWY−7208 superpathway of pyrimidine nucleobases salvage Treponema socranskii PWY−7184 pyrimidine deoxyribonucleotides de novo biosynthesis I PWY−6703 preQ0 biosynthesis Treponema medium PWY−2941 L−lysine biosynthesis II MET−SAM−PWY superpathway of S−adenosyl−L−methionine biosynthesis Prevotella pleuritidis METSYN−PWY L−homoserine and L−methionine biosynthesis PWY−7220 adenosine deoxyribonucleotides de novo biosynthesis II PWY−7222 guanosine deoxyribonucleotides de novo biosynthesis II Prevotella intermedia DENOVOPURINE2−PWY superpathway of purine nucleotides de novo biosynthesis II PWY−7187 pyrimidine deoxyribonucleotides de novo biosynthesis II Mycoplasma orale PWY−6270 isoprene biosynthesis I PWY−7560 methylerythritol phosphate pathway II Riemerella unclassified ANAGLYCOLYSIS−PWY glycolysis III (from glucose) PWY−5188 tetrapyrrole biosynthesis I (from glutamate) Neisseria elongata CALVIN−PWY Calvin−Benson−Bassham cycle PWY−7282 4−amino−2−methyl−5−phosphomethylpyrimidine biosynthesis (yeast) Kingella denitrificans PWY−6123 inosine−5'−phosphate biosynthesis I PWY−6124 inosine−5'−phosphate biosynthesis II THISYNARA−PWY superpathway of thiamin diphosphate biosynthesis III (eukaryotes) Alloprevotella unclassified PYRIDNUCSYN−PWY NAD biosynthesis I (from aspartate) PWY−5899 superpathway of menaquinol−13 biosynthesis Escherichia coli PWY−5897 superpathway of menaquinol−11 biosynthesis PWY−5898 superpathway of menaquinol−12 biosynthesis Abiotrophia defectiva PWY66−409 superpathway of purine nucleotide salvage PWY−6897 thiamin salvage II Gemella morbillorum PWY−7357 thiamin formation from pyrithiamine and oxythiamine (yeast) Log Abundance PWY−5971 palmitate biosynthesis II (bacteria and plants) Log Abundance Gemella haemolysans PWYG−321 mycolate biosynthesis PWY−5840 superpathway of menaquinol−7 biosynthesis PWY0−1586 peptidoglycan maturation (meso−diaminopimelate containing) Streptococcus intermedius PWY−5791 1,4−dihydroxy−2−naphthoate biosynthesis II (plants) 3 6 PWY−5837 1,4−dihydroxy−2−naphthoate biosynthesis I Prevotella oulorum COBALSYN−PWY adenosylcobalamin salvage from cobinamide I PWY−6608 guanosine nucleotides degradation III Campylobacter concisus PWY0−1297 superpathway of purine deoxyribonucleosides degradation PWY−4981 L−proline biosynthesis II (from arginine) Streptococcus salivarius GLYCOGENSYNTH−PWY glycogen biosynthesis I (from ADP−D−Glucose) 4 PWY−621 sucrose degradation III (sucrose invertase) 2 Streptococcus infantis PWY−1269 CMP−3−deoxy−D−manno−octulosonate biosynthesis I PWY−5989 stearate biosynthesis II (bacteria and plants) GLUTORN−PWY L−ornithine biosynthesis Capnocytophaga unclassified PWY−7539 6−hydroxymethyl−dihydropterin diphosphate biosynthesis III (Chlamydia) PWY0−781 aspartate superpathway 2 Streptococcus mitis oralis pneumoniae P4−PWY superpathway of L−lysine, L−threonine and L−methionine biosynthesis I 1 DAPLYSINESYN−PWY L−lysine biosynthesis I Oribacterium sinus PWY−6628 superpathway of L−phenylalanine biosynthesis HISTSYN−PWY L−histidine biosynthesis Fusobacterium nucleatum PWY−6527 stachyose degradation HOMOSER−METSYN−PWY L−methionine biosynthesis I 0 Granulicatella adiacens HSERMETANA−PWY L−methionine biosynthesis III 0 PWY4FS−7 phosphatidylglycerol biosynthesis I (plastidic) PWY4FS−8 phosphatidylglycerol biosynthesis II (non−plastidic) Granulicatella unclassified HEME−BIOSYNTHESIS−II heme biosynthesis I (aerobic) PWY−7400 L−arginine biosynthesis IV (archaebacteria) Rothia dentocariosa ARGSYN−PWY L−arginine biosynthesis I (via L−ornithine) PWY−6471 peptidoglycan biosynthesis IV (Enterococcus faecium) Rothia aeria OANTIGEN−PWY O−antigen building blocks biosynthesis (E. coli) UDPNAGSYN−PWY UDP−N−acetyl−D−glucosamine biosynthesis I Leptotrichia unclassified PENTOSE−P−PWY pentose phosphate pathway PWY0−1261 anhydromuropeptides recycling LACTOSECAT−PWY lactose and galactose degradation I Actinomyces graevenitzii GLCMANNANAUT−PWY superpathway of N−acetylglucosamine, N−acetylmannosamine and N−acetylneuraminate degradation PWY0−845 superpathway of pyridoxal 5'−phosphate biosynthesis and salvage Actinomyces odontolyticus PYRIDOXSYN−PWY pyridoxal 5'−phosphate biosynthesis I PWY66−399 gluconeogenesis III Porphyromonas catoniae PWY−7383 anaerobic energy metabolism (invertebrates, cytosol) ARGSYNBSUB−PWY L−arginine biosynthesis II (acetyl cycle) Peptostreptococcus stomatis PWY−5154 L−arginine biosynthesis III (via N−acetyl−L−citrulline) PWY−5121 superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) Peptostreptococcus unclassified HEXITOLDEGSUPER−PWY superpathway of hexitol degradation (bacteria) P185−PWY formaldehyde assimilation III (dihydroxyacetone cycle) NAD−BIOSYNTHESIS−II NAD salvage pathway II Porphyromonas sp oral taxon 279 PWY−5030 L−histidine degradation III PWY−5913 TCA cycle VI (obligate autotrophs) Prevotella histicola FERMENTATION−PWY mixed acid fermentation GLYCOLYSIS−E−D superpathway of glycolysis and Entner−Doudoroff Prevotella melaninogenica P441−PWY superpathway of N−acetylneuraminate degradation PWY−5659 GDP−mannose biosynthesis Veillonella unclassified NAGLIPASYN−PWY lipid IVA biosynthesis P42−PWY incomplete reductive TCA cycle Prevotella salivae PWY−6901 superpathway of glucose and xylose degradation BIOTIN−BIOSYNTHESIS−PWY biotin biosynthesis I PWY−6519 8−amino−7−oxononanoate biosynthesis I Prevotella pallens TCA TCA cycle I (prokaryotic) HISDEG−PWY L−histidine degradation I Granulicatella elegans PWY−922 mevalonate pathway I PWY−3781 aerobic respiration I (cytochrome c) candidate division TM7 TM7c PWY−5920 superpathway of heme biosynthesis from glycine PWY0−1415 superpathway of heme biosynthesis from uroporphyrinogen−III candidate division TM7 TM7b P164−PWY purine nucleobases degradation I (anaerobic) PWY−6545 pyrimidine deoxyribonucleotides de novo biosynthesis III Megasphaera micronuciformis POLYAMSYN−PWY superpathway of polyamine biosynthesis I PWY−5005 biotin biosynthesis II ARG+POLYAMINE−SYN superpathway of arginine and polyamine biosynthesis Neisseria unclassified GLUCONEO−PWY gluconeogenesis I PWY0−1298 superpathway of pyrimidine deoxyribonucleosides degradation Rothia mucilaginosa PWY−7117 C4 photosynthetic carbon assimilation cycle, PEPCK type PWY−7115 C4 photosynthetic carbon assimilation cycle, NAD−ME type Haemophilus parainfluenzae PWY−6284 superpathway of unsaturated fatty acids biosynthesis (E. coli) PWY−6285 superpathway of fatty acids biosynthesis (E. coli) Streptococcus sanguinis PWY−6113 superpathway of mycolate biosynthesis THISYN−PWY superpathway of thiamin diphosphate biosynthesis I Veillonella parvula PWY−6895 superpathway of thiamin diphosphate biosynthesis II PWY−6969 TCA cycle V (2−oxoglutarateferredoxin oxidoreductase) PYRIDNUCSAL−PWY NAD salvage pathway I Solobacterium moorei PWY−241 C4 photosynthetic carbon assimilation cycle, NADP−ME type PWY−7456 mannan degradation Atopobium parvulum PWY−7279 aerobic respiration II (cytochrome c) (yeast) PWY0−1479 tRNA processing Streptococcus parasanguinis PWY−5345 superpathway of L−methionine biosynthesis (by sulfhydrylation) SULFATE−CYS−PWY superpathway of sulfate assimilation and cysteine biosynthesis Veillonella atypica METHGLYUT−PWY superpathway of methylglyoxal degradation PWY−5083 NAD/NADH phosphorylation and dephosphorylation Veillonella dispar PWY0−1241 ADP−L−glycero−β−D−manno−heptose biosynthesis SO4ASSIM−PWY sulfate reduction I (assimilatory) PWY−6803 phosphatidylcholine acyl editing Eubacterium infirmum P161−PWY acetylene degradation PWY−5384 sucrose degradation IV (sucrose phosphorylase) Fusobacterium periodonticum PWY−6606 guanosine nucleotides degradation II PWY−6595 superpathway of guanosine nucleotides degradation (plants) Prevotella nanceiensis PWY−5676 acetyl−CoA fermentation to butanoate II FOLSYN−PWY superpathway of tetrahydrofolate biosynthesis and salvage Human herpesvirus 7 PWY−6612 superpathway of tetrahydrofolate biosynthesis P163−PWY L−lysine fermentation to acetate and butanoate Neisseria flavescens P122−PWY heterolactic fermentation PWY−5173 superpathway of acetyl−CoA biosynthesis PWY−6859 all−trans−farnesol biosynthesis Gemella sanguinis POLYISOPRENSYN−PWY polyisoprenoid biosynthesis (E. coli) GOLPDLCAT−PWY superpathway of glycerol degradation to 1,3−propanediol Streptococcus australis P461−PWY hexitol fermentation to lactate, formate, ethanol and acetate PWY−6263 superpathway of menaquinol−8 biosynthesis II Lachnospiraceae bacterium ICM7 PWY−5838 superpathway of menaquinol−8 biosynthesis I PWY−5861 superpathway of demethylmenaquinol−8 biosynthesis Streptococcus cristatus PWY−821 superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) PWY−7392 taxadiene biosynthesis (engineered) Selenomonas noxia PWY−5863 superpathway of phylloquinol biosynthesis PWY−5910 superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) RHAMCAT−PWY L−rhamnose degradation I Prevotella maculosa PWY−5367 petroselinate biosynthesis PWY−6353 purine nucleotides degradation II (aerobic) Stomatobaculum longum SALVADEHYPOX−PWY adenosine nucleotides degradation II PPGPPMET−PWY ppGpp biosynthesis Actinomyces viscosus GLUCOSE1PMETAB−PWY glucose and glucose−1−phosphate degradation PWY−7013 L−1,2−propanediol degradation Catonella morbi PWY1F−823 leucopelargonidin and leucocyanidin biosynthesis PWY−7237 myo−, chiro− and scillo−inositol degradation Capnocytophaga ochracea GLYCOL−GLYOXDEG−PWY superpathway of glycol metabolism and degradation TEICHOICACID−PWY teichoic acid (poly−glycerol) biosynthesis PWY−6562 norspermidine biosynthesis Corynebacterium matruchotii CITRULBIO−PWY L−citrulline biosynthesis PWY−4984 urea cycle Capnocytophaga gingivalis PWY−5675 nitrate reduction V (assimilatory) PWY−6748 nitrate reduction VII (denitrification) Campylobacter showae DENITRIFICATION−PWY nitrate reduction I (denitrification) PRPP−PWY superpathway of histidine, purine, and pyrimidine biosynthesis Haemophilus haemolyticus PWY−7196 superpathway of pyrimidine ribonucleosides salvage P108−PWY pyruvate fermentation to propanoate I Haemophilus influenzae POLYAMINSYN3−PWY superpathway of polyamine biosynthesis II PWY−5088 L−glutamate degradation VIII (to propanoate) ARGININE−SYN4−PWY L−ornithine de novo biosynthesis Lautropia mirabilis ARGORNPROST−PWY arginine, ornithine and proline interconversion PWY−5101 L−isoleucine biosynthesis II Neisseria sicca PWY66−398 TCA cycle III (animals) PWY−6549 L−glutamine biosynthesis III Neisseria meningitidis PWY−7211 superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis PWY−7210 pyrimidine deoxyribonucleotides biosynthesis from CTP Leptotrichia wadei PWY−7198 pyrimidine deoxyribonucleotides de novo biosynthesis IV P124−PWY Bifidobacterium shunt Streptococcus gordonii PWY−7031 protein N−glycosylation (bacterial) PWY−6749 CMP−legionaminate biosynthesis I PWY−6892 thiazole biosynthesis I (E. coli) Selenomonas flueggei PWY−6891 thiazole biosynthesis II (Bacillus) PWY−4041 γ−glutamyl cycle Streptococcus tigurinus PWY−7268 NAD/NADP−NADH/NADPH cytosolic interconversion (yeast) PWY−7371 1,4−dihydroxy−6−naphthoate biosynthesis II Alloprevotella rava PWY−6305 putrescine biosynthesis IV GLYCOCAT−PWY glycogen degradation I (bacterial) Streptococcus constellatus REDCITCYC TCA cycle VIII (helicobacter) PWY−7254 TCA cycle VII (acetate−producers) Bacteroidetes oral taxon 274 PWY−5464 superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle PWY−5690 TCA cycle II (plants and fungi) PWY−4702 phytate degradation I Prevotella micans PWY−7242 D−fructuronate degradation GLUCUROCAT−PWY superpathway of β−D−glucuronide and D−glucuronate degradation Filifactor alocis PWY−6507 4−deoxy−L−threo−hex−4−enopyranuronate degradation GALACTUROCAT−PWY D−galacturonate degradation I Streptococcus mutans GALACT−GLUCUROCAT−PWY superpathway of hexuronide and hexuronate degradation GLYCOLYSIS−TCA−GLYOX−BYPASS superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass Human herpesvirus 4 TCA−GLYOX−BYPASS superpathway of glyoxylate bypass and TCA GLYOXYLATE−BYPASS glyoxylate cycle Cryptobacterium curtum P105−PWY TCA cycle IV (2−oxoglutarate decarboxylase) PWY−5723 Rubisco shunt FUCCAT−PWY fucose degradation Shuttleworthia satelles FUC−RHAMCAT−PWY superpathway of fucose and rhamnose degradation PWY66−389 phytol degradation Prevotella denticola P125−PWY superpathway of (R,R)−butanediol biosynthesis PWY1G−0 mycothiol biosynthesis Scardovia wiggsiae PWY−7431 aromatic biogenic amine degradation (bacteria) PWY−6708 ubiquinol−8 biosynthesis (prokaryotic) Dialister invisus PWY−5857 ubiquinol−10 biosynthesis (prokaryotic) PWY−5855 ubiquinol−7 biosynthesis (prokaryotic) Prevotella nigrescens PWY−5856 ubiquinol−9 biosynthesis (prokaryotic) GALACTARDEG−PWY D−galactarate degradation I GLUCARGALACTSUPER−PWY superpathway of D−glucarate and D−galactarate degradation Prevotella oris GLUCARDEG−PWY D−glucarate degradation I PWY−6823 molybdenum cofactor biosynthesis Prevotella veroralis PWY−6630 superpathway of L−tyrosine biosynthesis PWY−7269 NAD/NADP−NADH/NADPH mitochondrial interconversion (yeast) Atopobium rimae COLANSYN−PWY colanic acid building blocks biosynthesis PWY−7323 superpathway of GDP−mannose−derived O−antigen building blocks biosynthesis Alloprevotella tannerae PWY−5104 L−isoleucine biosynthesis IV PWY−6588 pyruvate fermentation to acetone Parvimonas micra PWY4LZ−257 superpathway of fermentation (Chlamydomonas reinhardtii) P23−PWY reductive TCA cycle I PWY−7003 glycerol degradation to butanol Parvimonas unclassified P162−PWY L−glutamate degradation V (via hydroxyglutarate) Eubacterium brachy PWY−5022 4−aminobutanoate degradation V SC43 SC45 SC19 SC44 SC30 SC23 SC42 SC50 SC35 SC17 SC41 SC49 SC46 SC51 SC48 SC56 SC55 SC54 SC33 SC24 SC29 SC53 SC47 SC28 SC39 SC16 SC36 SC38 SC21 SC07 SC27 SC10 SC01 SC40 SC11 SC05 SC09 SC26 SC20 SC37 SC15 SC22 SC32 SC34 SC25 SC18 SC31 SC39 SC07 SC36 SC38 SC11 SC01 SC10 SC27 SC22 SC20 SC21 SC05 SC15 SC16 SC40 SC32 SC25 SC18 SC34 SC09 SC37 SC26 SC31 SC33 SC56 SC30 SC48 SC46 SC23 SC24 SC17 SC54 SC55 SC51 SC28 SC45 SC44 SC42 SC53 SC19 SC29 SC41 SC50 SC47 SC43 SC49 SC35

Taxonomic abundance heatmap Functional abundance heatmap D (clr transformed) E (clr transformed) Caries Healthy Caries Healthy

PWY−7211 superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis Alloprevotella tannerae PWY−7210 pyrimidine deoxyribonucleotides biosynthesis from CTP PWY−7198 pyrimidine deoxyribonucleotides de novo biosynthesis IV Treponema medium PWY−6353 purine nucleotides degradation II (aerobic) SALVADEHYPOX−PWY adenosine nucleotides degradation II Treponema denticola PWY−5863 superpathway of phylloquinol biosynthesis PWY−7392 taxadiene biosynthesis (engineered) Eubacterium brachy PWY−5910 superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) PWY−7013 L−1,2−propanediol degradation Parvimonas unclassified CITRULBIO−PWY L−citrulline biosynthesis PWY−4984 urea cycle PWY66−399 gluconeogenesis III Parvimonas micra PWY−7383 anaerobic energy metabolism (invertebrates, cytosol) PWY0−1479 tRNA processing Scardovia wiggsiae PWY−6562 norspermidine biosynthesis P108−PWY pyruvate fermentation to propanoate I Prevotella denticola GLUCONEO−PWY gluconeogenesis I PWY−241 C4 photosynthetic carbon assimilation cycle, NADP−ME type Human herpesvirus 4 POLYAMINSYN3−PWY superpathway of polyamine biosynthesis II PWY−5088 L−glutamate degradation VIII (to propanoate) Filifactor alocis P162−PWY L−glutamate degradation V (via hydroxyglutarate) PWY−5022 4−aminobutanoate degradation V PWY−5104 L−isoleucine biosynthesis IV Streptococcus mutans PWY−6588 pyruvate fermentation to acetone PWY4LZ−257 superpathway of fermentation (Chlamydomonas reinhardtii) Cryptobacterium curtum P23−PWY reductive TCA cycle I PWY−7003 glycerol degradation to butanol Shuttleworthia satelles TEICHOICACID−PWY teichoic acid (poly−glycerol) biosynthesis FUCCAT−PWY fucose degradation Prevotella veroralis FUC−RHAMCAT−PWY superpathway of fucose and rhamnose degradation PWY−5675 nitrate reduction V (assimilatory) Atopobium rimae METHGLYUT−PWY superpathway of methylglyoxal degradation PWY1F−823 leucopelargonidin and leucocyanidin biosynthesis PWY−5173 superpathway of acetyl−CoA biosynthesis Dialister invisus P122−PWY heterolactic fermentation P161−PWY acetylene degradation Prevotella nigrescens PWY−5384 sucrose degradation IV (sucrose phosphorylase) HEXITOLDEGSUPER−PWY superpathway of hexitol degradation (bacteria) Prevotella oris P461−PWY hexitol fermentation to lactate, formate, ethanol and acetate PWY−6471 peptidoglycan biosynthesis IV (Enterococcus faecium) Alloprevotella rava GOLPDLCAT−PWY superpathway of glycerol degradation to 1,3−propanediol PWY−6606 guanosine nucleotides degradation II Streptococcus tigurinus PWY−6595 superpathway of guanosine nucleotides degradation (plants) PWY1G−0 mycothiol biosynthesis PWY−7431 aromatic biogenic amine degradation (bacteria) Granulicatella elegans PWY−5676 acetyl−CoA fermentation to butanoate II PWY−5920 superpathway of heme biosynthesis from glycine Haemophilus haemolyticus PWY0−1415 superpathway of heme biosynthesis from uroporphyrinogen−III POLYISOPRENSYN−PWY polyisoprenoid biosynthesis (E. coli) Neisseria meningitidis PWY−5121 superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) PWY−6859 all−trans−farnesol biosynthesis Aggregatibacter segnis PWY0−1261 anhydromuropeptides recycling PWY66−400 glycolysis VI (metazoan) Haemophilus influenzae GLYCOLYSIS glycolysis I (from glucose 6−phosphate) PWY−5484 glycolysis II (from fructose 6−phosphate) Neisseria sicca GLCMANNANAUT−PWY superpathway of N−acetylglucosamine, N−acetylmannosamine and N−acetylneuraminate degradation P441−PWY superpathway of N−acetylneuraminate degradation GLYCOLYSIS−E−D superpathway of glycolysis and Entner−Doudoroff Neisseria macacae FERMENTATION−PWY mixed acid fermentation PWY−7117 C4 photosynthetic carbon assimilation cycle, PEPCK type Kingella denitrificans PWY−5913 TCA cycle VI (obligate autotrophs) NAD−BIOSYNTHESIS−II NAD salvage pathway II Neisseria unclassified OANTIGEN−PWY O−antigen building blocks biosynthesis (E. coli) UDPNAGSYN−PWY UDP−N−acetyl−D−glucosamine biosynthesis I Capnocytophaga unclassified P185−PWY formaldehyde assimilation III (dihydroxyacetone cycle) PWY−5030 L−histidine degradation III Gemella morbillorum LACTOSECAT−PWY lactose and galactose degradation I PWY−922 mevalonate pathway I PWY−5918 superpathay of heme biosynthesis from glutamate Abiotrophia defectiva HEME−BIOSYNTHESIS−II heme biosynthesis I (aerobic) PWY−5188 tetrapyrrole biosynthesis I (from glutamate) Prevotella histicola PWY−5189 tetrapyrrole biosynthesis II (from glycine) RIBOSYN2−PWY flavin biosynthesis I (bacteria and plants) Megasphaera micronuciformis ANAGLYCOLYSIS−PWY glycolysis III (from glucose) ANAEROFRUCAT−PWY homolactic fermentation Stomatobaculum longum PENTOSE−P−PWY pentose phosphate pathway CALVIN−PWY Calvin−Benson−Bassham cycle Prevotella pallens NONOXIPENT−PWY pentose phosphate pathway (non−oxidative branch) PWY−6527 stachyose degradation PWY−6270 isoprene biosynthesis I Eubacterium infirmum PWY−7560 methylerythritol phosphate pathway II PWY0−1296 purine ribonucleosides degradation Actinomyces odontolyticus PWY−5100 pyruvate fermentation to acetate and lactate II PWY−6121 5−aminoimidazole ribonucleotide biosynthesis I Streptococcus mitis oralis pneumoniae PWY−6122 5−aminoimidazole ribonucleotide biosynthesis II PWY−6277 superpathway of 5−aminoimidazole ribonucleotide biosynthesis Gemella haemolysans 1CMET2−PWY N10−formyl−tetrahydrofolate biosynthesis PWY−5347 superpathway of L−methionine biosynthesis (transsulfuration) Haemophilus parainfluenzae HOMOSER−METSYN−PWY L−methionine biosynthesis I MET−SAM−PWY superpathway of S−adenosyl−L−methionine biosynthesis METSYN−PWY L−homoserine and L−methionine biosynthesis Oribacterium sinus PWY−7111 pyruvate fermentation to isobutanol (engineered) ILEUSYN−PWY L−isoleucine biosynthesis I (from threonine) Veillonella unclassified VALSYN−PWY L−valine biosynthesis HSERMETANA−PWY L−methionine biosynthesis III Streptococcus sanguinis PWY−3001 superpathway of L−isoleucine biosynthesis I THRESYN−PWY superpathway of L−threonine biosynthesis Campylobacter concisus BRANCHED−CHAIN−AA−SYN−PWY superpathway of branched amino acid biosynthesis PWY−5103 L−isoleucine biosynthesis III Fusobacterium nucleatum PWY−6703 preQ0 biosynthesis PWY−7208 superpathway of pyrimidine nucleobases salvage Granulicatella adiacens PWY−7197 pyrimidine deoxyribonucleotide phosphorylation PWY0−166 superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli) PWY−6125 superpathway of guanosine nucleotides de novo biosynthesis II Streptococcus intermedius PWY−7228 superpathway of guanosine nucleotides de novo biosynthesis I PWY−7184 pyrimidine deoxyribonucleotides de novo biosynthesis I Prevotella melaninogenica PWY−6936 seleno−amino acid biosynthesis PWY0−1061 superpathway of L−alanine biosynthesis Veillonella parvula PWY−7234 inosine−5'−phosphate biosynthesis III PWY−3841 folate transformations II Solobacterium moorei PWY−2941 L−lysine biosynthesis II PWY66−422 D−galactose degradation V (Leloir pathway) Atopobium parvulum PWY−6317 galactose degradation I (Leloir pathway) GLUTORN−PWY L−ornithine biosynthesis HEMESYN2−PWY heme biosynthesis II (anaerobic) Streptococcus parasanguinis PWY−7400 L−arginine biosynthesis IV (archaebacteria) ARGSYN−PWY L−arginine biosynthesis I (via L−ornithine) clr(Abundance) Streptococcus salivarius HISTSYN−PWY L−histidine biosynthesis PHOSLIPSYN−PWY superpathway of phospholipid biosynthesis I (bacteria) Prevotella salivae PWY4FS−7 phosphatidylglycerol biosynthesis I (plastidic) PWY4FS−8 phosphatidylglycerol biosynthesis II (non−plastidic) Prevotella oulorum PWY−6901 superpathway of glucose and xylose degradation 10 TCA TCA cycle I (prokaryotic) Veillonella atypica HISDEG−PWY L−histidine degradation I PWY−3781 aerobic respiration I (cytochrome c) clr(Abundance) PWY−7279 aerobic respiration II (cytochrome c) (yeast) Veillonella dispar ARGSYNBSUB−PWY L−arginine biosynthesis II (acetyl cycle) PWY−5154 L−arginine biosynthesis III (via N−acetyl−L−citrulline) 5 Leptotrichia unclassified PWY−6803 phosphatidylcholine acyl editing 10 SO4ASSIM−PWY sulfate reduction I (assimilatory) Selenomonas flueggei PWY−5345 superpathway of L−methionine biosynthesis (by sulfhydrylation) SULFATE−CYS−PWY superpathway of sulfate assimilation and cysteine biosynthesis Leptotrichia wadei GLYCOL−GLYOXDEG−PWY superpathway of glycol metabolism and degradation GLUCOSE1PMETAB−PWY glucose and glucose−1−phosphate degradation 0 Selenomonas sputigena PWY−5083 NAD/NADH phosphorylation and dephosphorylation PWY0−162 superpathway of pyrimidine ribonucleotides de novo biosynthesis 5 DAPLYSINESYN−PWY L−lysine biosynthesis I Streptococcus gordonii P4−PWY superpathway of L−lysine, L−threonine and L−methionine biosynthesis I PWY0−781 aspartate superpathway −5 Lachnospiraceae bacterium oral taxon 082 PWY−7539 6−hydroxymethyl−dihydropterin diphosphate biosynthesis III (Chlamydia) NAGLIPASYN−PWY lipid IVA biosynthesis Lachnoanaerobaculum saburreum PWY0−1241 ADP−L−glycero−β−D−manno−heptose biosynthesis 0 PWY−5659 GDP−mannose biosynthesis Bacteroidetes oral taxon 274 PWY−6168 flavin biosynthesis III (fungi) P42−PWY incomplete reductive TCA cycle −10 Prevotella micans PWY−6748 nitrate reduction VII (denitrification) DENITRIFICATION−PWY nitrate reduction I (denitrification) candidate division TM7 TM7c PWY−7237 myo−, chiro− and scillo−inositol degradation −5 PWY0−845 superpathway of pyridoxal 5'−phosphate biosynthesis and salvage PYRIDOXSYN−PWY pyridoxal 5'−phosphate biosynthesis I candidate division TM7 TM7b BIOTIN−BIOSYNTHESIS−PWY biotin biosynthesis I PWY−6519 8−amino−7−oxononanoate biosynthesis I Porphyromonas catoniae P163−PWY L−lysine fermentation to acetate and butanoate PPGPPMET−PWY ppGpp biosynthesis Prevotella saccharolytica PWY−5723 Rubisco shunt ARGININE−SYN4−PWY L−ornithine de novo biosynthesis Alloprevotella unclassified ARGORNPROST−PWY arginine, ornithine and proline interconversion PWY−821 superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) Escherichia coli P105−PWY TCA cycle IV (2−oxoglutarate decarboxylase) GLYOXYLATE−BYPASS glyoxylate cycle GLYCOLYSIS−TCA−GLYOX−BYPASS superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass Porphyromonas endodontalis TCA−GLYOX−BYPASS superpathway of glyoxylate bypass and TCA PWY−6263 superpathway of menaquinol−8 biosynthesis II Prevotella intermedia PWY−5838 superpathway of menaquinol−8 biosynthesis I PWY−5861 superpathway of demethylmenaquinol−8 biosynthesis Mycoplasma orale PWYG−321 mycolate biosynthesis PWY−6113 superpathway of mycolate biosynthesis Streptococcus constellatus PWY−5971 palmitate biosynthesis II (bacteria and plants) PWY−5367 petroselinate biosynthesis Prevotella pleuritidis PWY−6285 superpathway of fatty acids biosynthesis (E. coli) PWY−6284 superpathway of unsaturated fatty acids biosynthesis (E. coli) GLYCOCAT−PWY glycogen degradation I (bacterial) Human herpesvirus 7 PWY−5690 TCA cycle II (plants and fungi) PWY−5464 superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle Streptococcus cristatus REDCITCYC TCA cycle VIII (helicobacter) PWY−7254 TCA cycle VII (acetate−producers) Streptococcus oligofermentans PWY−7242 D−fructuronate degradation GLUCUROCAT−PWY superpathway of β−D−glucuronide and D−glucuronate degradation Streptococcus australis PWY−6507 4−deoxy−L−threo−hex−4−enopyranuronate degradation GALACTUROCAT−PWY D−galacturonate degradation I Lachnospiraceae bacterium ICM7 GALACT−GLUCUROCAT−PWY superpathway of hexuronide and hexuronate degradation PWY−4702 phytate degradation I PWY−6545 pyrimidine deoxyribonucleotides de novo biosynthesis III Gemella sanguinis PWY−7456 mannan degradation PWY−6630 superpathway of L−tyrosine biosynthesis Prevotella nanceiensis PWY−7269 NAD/NADP−NADH/NADPH mitochondrial interconversion (yeast) COLANSYN−PWY colanic acid building blocks biosynthesis Fusobacterium periodonticum PWY−7323 superpathway of GDP−mannose−derived O−antigen building blocks biosynthesis PWY−6823 molybdenum cofactor biosynthesis Streptococcus infantis GLUCARDEG−PWY D−glucarate degradation I PWY−6708 ubiquinol−8 biosynthesis (prokaryotic) Streptococcus peroris PWY−5857 ubiquinol−10 biosynthesis (prokaryotic) PWY−5855 ubiquinol−7 biosynthesis (prokaryotic) Corynebacterium matruchotii PWY−5856 ubiquinol−9 biosynthesis (prokaryotic) GALACTARDEG−PWY D−galactarate degradation I GLUCARGALACTSUPER−PWY superpathway of D−glucarate and D−galactarate degradation Lachnospiraceae oral taxon 107 THISYN−PWY superpathway of thiamin diphosphate biosynthesis I PWY−6892 thiazole biosynthesis I (E. coli) Leptotrichia hofstadii PWY−6895 superpathway of thiamin diphosphate biosynthesis II PWY−6891 thiazole biosynthesis II (Bacillus) Actinomyces johnsonii PWY−5101 L−isoleucine biosynthesis II PWY66−398 TCA cycle III (animals) Capnocytophaga granulosa PWY−6549 L−glutamine biosynthesis III PWY−6749 CMP−legionaminate biosynthesis I Cardiobacterium hominis FOLSYN−PWY superpathway of tetrahydrofolate biosynthesis and salvage PWY−6612 superpathway of tetrahydrofolate biosynthesis PWY−6969 TCA cycle V (2−oxoglutarateferredoxin oxidoreductase) Propionibacterium propionicum PYRIDNUCSAL−PWY NAD salvage pathway I PWY−6628 superpathway of L−phenylalanine biosynthesis Eubacterium yurii RHAMCAT−PWY L−rhamnose degradation I PWY66−389 phytol degradation Selenomonas artemidis P164−PWY purine nucleobases degradation I (anaerobic) PWY−7282 4−amino−2−methyl−5−phosphomethylpyrimidine biosynthesis (yeast) Catonella morbi PWY−6123 inosine−5'−phosphate biosynthesis I PWY−6124 inosine−5'−phosphate biosynthesis II Capnocytophaga ochracea PWY−7220 adenosine deoxyribonucleotides de novo biosynthesis II PWY−7222 guanosine deoxyribonucleotides de novo biosynthesis II PWY−7229 superpathway of adenosine nucleotides de novo biosynthesis I Selenomonas noxia PWY−6126 superpathway of adenosine nucleotides de novo biosynthesis II TRPSYN−PWY L−tryptophan biosynthesis Prevotella maculosa PWY−621 sucrose degradation III (sucrose invertase) PWY−6897 thiamin salvage II Selenomonas infelix PWY−7357 thiamin formation from pyrithiamine and oxythiamine (yeast) PWY0−1319 CDP−diacylglycerol biosynthesis II Oribacterium sp oral taxon 078 PWY−5667 CDP−diacylglycerol biosynthesis I PWY−841 superpathway of purine nucleotides de novo biosynthesis I Campylobacter gracilis DENOVOPURINE2−PWY superpathway of purine nucleotides de novo biosynthesis II PWY−7187 pyrimidine deoxyribonucleotides de novo biosynthesis II PWY−5005 biotin biosynthesis II Leptotrichia buccalis PWY−5899 superpathway of menaquinol−13 biosynthesis PWY−5897 superpathway of menaquinol−11 biosynthesis Candidatus Prevotella conceptionensis PWY−5898 superpathway of menaquinol−12 biosynthesis PWY−5791 1,4−dihydroxy−2−naphthoate biosynthesis II (plants) Prevotella loescheii PWY−5837 1,4−dihydroxy−2−naphthoate biosynthesis I ARG+POLYAMINE−SYN superpathway of arginine and polyamine biosynthesis Treponema socranskii POLYAMSYN−PWY superpathway of polyamine biosynthesis I P125−PWY superpathway of (R,R)−butanediol biosynthesis Leptotrichia goodfellowii PWY−7115 C4 photosynthetic carbon assimilation cycle, NAD−ME type ASPASN−PWY superpathway of L−aspartate and L−asparagine biosynthesis Actinobacillus unclassified DTDPRHAMSYN−PWY dTDP−L−rhamnose biosynthesis I PWY−5973 cis−vaccenate biosynthesis PWY−7663 gondoate biosynthesis (anaerobic) Aggregatibacter aphrophilus PWY−6147 6−hydroxymethyl−dihydropterin diphosphate biosynthesis I PANTOSYN−PWY pantothenate and coenzyme A biosynthesis I Escherichia unclassified PANTO−PWY phosphopantothenate biosynthesis I PWY−6700 queuosine biosynthesis Haemophilus paraphrohaemolyticus NONMEVIPP−PWY methylerythritol phosphate pathway I PWY−5686 UMP biosynthesis Neisseria elongata PWY−1042 glycolysis IV (plant cytosol) PWY−6385 peptidoglycan biosynthesis III (mycobacteria) Lautropia mirabilis PWY0−1586 peptidoglycan maturation (meso−diaminopimelate containing) PWY−5097 L−lysine biosynthesis VI PWY−724 superpathway of L−lysine, L−threonine and L−methionine biosynthesis II Capnocytophaga gingivalis PWY−7199 pyrimidine deoxyribonucleosides salvage COA−PWY coenzyme A biosynthesis I Campylobacter showae PWY−4242 pantothenate and coenzyme A biosynthesis III COA−PWY−1 coenzyme A biosynthesis II (mammalian) Actinomyces naeslundii PWY−6163 chorismate biosynthesis from 3−dehydroquinate ARO−PWY chorismate biosynthesis I Eikenella corrodens COMPLETE−ARO−PWY superpathway of aromatic amino acid biosynthesis PWY−6151 S−adenosyl−L−methionine cycle I Actinomyces oris PWY−2942 L−lysine biosynthesis III PWY−7219 adenosine ribonucleotides de novo biosynthesis PWY−7221 guanosine ribonucleotides de novo biosynthesis Aggregatibacter unclassified PEPTIDOGLYCANSYN−PWY peptidoglycan biosynthesis I (meso−diaminopimelate containing) PWY−6386 UDP−N−acetylmuramoyl−pentapeptide biosynthesis II (lysine−containing) Corynebacterium durum PWY−6387 UDP−N−acetylmuramoyl−pentapeptide biosynthesis I (meso−diaminopimelate containing) PWY66−409 superpathway of purine nucleotide salvage Actinomyces massiliensis PWY0−1297 superpathway of purine deoxyribonucleosides degradation PWY−4981 L−proline biosynthesis II (from arginine) Granulicatella unclassified PWY−6609 adenine and adenosine salvage III PWY−5695 urate biosynthesis/inosine 5'−phosphate degradation Rothia dentocariosa PWY−6737 starch degradation V TRNA−CHARGING−PWY tRNA charging GLYCOGENSYNTH−PWY glycogen biosynthesis I (from ADP−D−Glucose) Rothia mucilaginosa PWY−1269 CMP−3−deoxy−D−manno−octulosonate biosynthesis I PWY−5989 stearate biosynthesis II (bacteria and plants) Rothia aeria PWY0−862 (5Z)−dodec−5−enoate biosynthesis PWY−6282 palmitoleate biosynthesis I (from (5Z)−dodec−5−enoate) Actinomyces graevenitzii FASYN−ELONG−PWY fatty acid elongation −− saturated PWY−7664 oleate biosynthesis IV (anaerobic) Actinomyces viscosus FASYN−INITIAL−PWY superpathway of fatty acid biosynthesis initiation (E. coli) PWY−7388 octanoyl−[acyl−carrier protein] biosynthesis (mitochondria, yeast) Riemerella unclassified PWY−5840 superpathway of menaquinol−7 biosynthesis PWY−6608 guanosine nucleotides degradation III COBALSYN−PWY adenosylcobalamin salvage from cobinamide I Peptostreptococcus stomatis PWY0−1298 superpathway of pyrimidine deoxyribonucleosides degradation PYRIDNUCSYN−PWY NAD biosynthesis I (from aspartate) Peptostreptococcus unclassified SER−GLYSYN−PWY superpathway of L−serine and glycine biosynthesis I THISYNARA−PWY superpathway of thiamin diphosphate biosynthesis III (eukaryotes) Porphyromonas sp oral taxon 279 PWY−4041 γ−glutamyl cycle PWY−7268 NAD/NADP−NADH/NADPH cytosolic interconversion (yeast) Haemophilus sputorum PWY−7031 protein N−glycosylation (bacterial) PWY−7371 1,4−dihydroxy−6−naphthoate biosynthesis II Neisseria flavescens PWY−6305 putrescine biosynthesis IV P124−PWY Bifidobacterium shunt Neisseria subflava PRPP−PWY superpathway of histidine, purine, and pyrimidine biosynthesis PWY−7196 superpathway of pyrimidine ribonucleosides salvage SC36 SC22 SC34 SC31 SC54 SC24 SC19 SC30 SC42 SC16 SC38 SC26 SC21 SC07 SC01 SC09 SC15 SC32 SC47 SC55 SC33 SC50 SC48 SC45 SC44 SC23 SC20 SC27 SC10 SC40 SC39 SC11 SC05 SC37 SC18 SC25 SC28 SC29 SC35 SC17 SC41 SC49 SC53 SC43 SC46 SC51 SC56 SC37 SC26 SC31 SC18 SC34 SC09 SC40 SC32 SC25 SC33 SC56 SC30 SC48 SC46 SC23 SC24 SC17 SC54 SC55 SC51 SC28 SC45 SC44 SC42 SC53 SC19 SC29 SC41 SC50 SC47 SC43 SC49 SC35 SC39 SC07 SC36 SC38 SC11 SC01 SC10 SC27 SC22 SC20 SC21 SC05 SC15 SC16 Supplemental Fig. S4: (A) Species abundance. Phylogenetic tree illustrating the species present across the saliva metagenomes. The relative abundance of each taxa is represented by the bar graph at the end of each leaf, with the relative abundance in the healthy group in blue and the caries group in red. Taxa of interest are highlighted with colored leaves on the tree:

Streptococcus mutans and Streptococcus sobrinus = yellow; Prevotella spp.= red; and Rothia spp. = green. (B) Heatmap illustrating species-level taxonomic abundances in the caries versus healthy groups. Plot was generated using the ComplexHeatmaps R package (Gu et al.

2016). Abundances were determined using MetaPhAn2 (Truong et al. 2015). Rows and columns were clustered using a Bray-Curtis distance matrix and the “complete” clustering method. Only taxa appearing in at least 10 samples are included in this figure. (C) Heatmap illustrating species-level functional pathway abundances in the caries versus healthy groups. Plot was generated using the ComplexHeatmaps R package (Gu et al. 2016). Abundances were determined using HumanN2 (Franzosa et al. 2018). Rows and columns were clustered using a

Bray-Curtis distance matrix and the “complete” clustering method. Only pathways included in at least 10 samples are included in this figure. (D) Heatmap illustrating centered log ratio (clr)- transformed species-level taxonomic abundances in the caries versus healthy groups.

Same data as panel B except the data is clr-transformed (as is performed in DEICODE). (E)

Heatmap illustrating clr-transformed functional pathway abundances in the caries versus healthy groups. Same data as panel C except the data is clr-transformed (as is performed in

DEICODE).

Figure S5

A Contributional diversity: B ARGSYN-PWY: L-arginine biosynthesis I (via L-ornithine) Contributional diversity: Stratifications: Stratifications: 140 PWY-7279: aerobic respiration II Veillonella dispar 80 Neisseria sicca 120 Veillonella parvula 70 Neisseria subflava Neisseria sicca Lautropia mirabilis 100 Neisseria flavescens 60 Neisseria flavescens 80 Lautropia mirabilis 50 Neisseria macacae Escherichia coli Campylobacter showae 40 60 Actinomyces viscosus Kingella denitrificans Other 30 Other 40

Relative abundance Unclassified Unclassified Relative abundance 20 20 10 Sample label: Sample label: caries 0 caries 0 healthy healthy Samples (N=47) Samples (N=47)

C Contributional diversity: D BRANCHED-CHAIN-AA-SYN-PWY: superpathway of branched amino acid biosynthesis Stratifications: PWY-4984: urea cycle 300 Streptococcus mitis oralis pneumoniae 17.5 Fusobacterium periodonticum 250 15.0 Stratifications: Streptococcus sanguinis Lautropia mirabilis 200 Streptococcus infantis 12.5 Propionibacterium propionicum Streptococcus parasanguinis Moraxella catarrhalis 10.0 150 Selenomonas flueggei Acidovorax ebreus Neisseria sicca 7.5 Treponema socranskii 100 Other Sample label: Relative abundance Unclassified 5.0 Relative abundance 50 caries 2.5 Sample label: healthy 0 caries 0.0 healthy Samples (N=47) Samples (N=47) Supplemental Fig. S5: Contributional diversity of functional pathways of interest in caries versus health. Stacked bar chart illustrating the relative abundance and contributional diversity of arginine biosynthesis across the samples. (A) Arginine synthesis via L-ornithine (B) Aerobic respiration (C) Branched-chain amino acid biosynthesis (D) Urea cycle.

Figure S6 A B iRep: all taxa iRep 2.4 2.5 Healthy 2.2 Caries 2.0 2.0 Re p

i 1.8 Re p i 1.6 1.5 1.4

1.2 1.0 Healthy Caries

Solobacterium Eubacterium suci PrevotellaPrevotella pallens salivae Prevotella histicola Prevotella sp. ICM33 Atopobium sp. ICM42b

Porphyromonadaceae KA00676 C Axis 2 (32.33 %) Porphyromonas sp. oral taxon 279 “Ca. Nanosynbacter GGB3” Porphyromonas sp. KLE 1280 “Ca. Nanosynbacter UMGS1926” Ca. Gracilibacteria FGB1

“Ca. Nanosynbacter GGB4”

Eubacterium sulci

Prevotella pallens Rothia sp. HMSC073B08 Prevotella melaninogenica Rothia sp. HMSC065C03 Prevotella sp. ICM33 Rothia sp. HMSC069C10 Scardovia wiggsiae

Prevotella salivae Veillonella dispar Rothia sp. HMSC068F09

Veillonella sp. HPA0037 Megasphaera micronuciformis Prevotella histicola Axis 1 (61.58 %) Permanova (Caries vs. Healthy): p = 0.011 Supplemental Fig. S6: iRep and genome-based taxonomic abundance. Replication rates of all taxa (A) and most abundant taxonomic groups (B). Replication rates were determined using iRep (Brown et al. 2016). Replication rates were not significantly different between healthy and caries groups for any taxonomic groups shown here for overall (A). (C) Beta diversity of taxa using quantification of assembled genome bins. 3D PCA plot generated using

DEICODE (robust Aitchison PCA) (Martino et al. 2019). Data points represent individual subjects and are colored with a gradient to visualize DMFT score, indicating severity of dental caries.

Feature loadings (i.e. taxa driving differences in ordination space) are illustrated by the vectors, which are labeled with the cognate species name.

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