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Dialister propionicifaciens Dialister sp. type 2 Dialister Dialisterpropionicifaciens propionicifaciens Dialister propionicifaciens Dialister propionicifaciens propionicifaciens Dialister Dialister succinatiphilus Dialister pneumosintes Dialister Supplementary Figure 3A Dialister micraerophilus Veillonellaceae Megasphaera micronuciformis MegasphaeraMegasphaera sp. type 2 Megasphaera sp. type 1 Firmicutes Veillonella montpellierensis VeillonellaVeillonella Veillonella atypica atypica Veillonella parvula Veillonella atypica BVAB2 BVAB3 Fastidiosipila sanguinis Faecalibacterium prausnitzii Bacteroides galacturonicusEubacterium siraeum Eubacterium eligens Dorea longicatena Moryella indoligenes Ruminococcus obeum Clostridiales Eubacterium rectale Roseburia faecis Roseburia hominis Roseburia intestinalis Roseburia inulinivorans Clostridiales Roseburia BVAB1 Eubacterium ramulusShuttleworthia satelles Catonella morbi Howardella ureilytica Candidatus Peptoniphilus massiliensis Bacteroides coagulans Peptoniphilus asaccharolyticus Peptoniphilus indolicus Peptoniphilus duerdenii Peptoniphilus Peptoniphilus harei Peptoniphilus lacrimalis Parvimonas micra Clostridiales Family XI. Incertae Sedis Finegoldia magna Anaerococcus hydrogenalis Anaerococcus vaginalis AnaerococcusAnaerococcus octavius Anaerococcus lactolyticus murdochii Anaerococcus Anaerococcus tetradius Anaerococcus prevotii Eubacterium saphenum Clostridium colicanis Peptostreptococcus anaerobius Peptostreptococcus Peptostreptococcus stomatis Mycoplasma hominis Clostridiales Ureaplasma parvum Ureaplasma Ureaplasma urealyticum Ureaplasma parvum parvum Ureaplasma Ureaplasma parvum Mycoplasma genitalium Mycoplasmataceae Enterococcus faecium Enterococcus durans Enterococcus durans Enterococcus Enterococcus avium Enterococcus faecalis Streptococcus parasanguinis Streptococcus agalactiae Streptococcus oralis Streptococcus mitis Streptococcus Streptococcusintermedius intermedius Streptococcus intermedius Streptococcus constellatus Streptococcus anginosus group Streptococcus intermedius Streptococcus intermedius Streptococcus anginosus Streptococcus Streptococcus mutans Streptococcus salivarius Streptococcus thermophilus Streptococcus salivarius salivarius Streptococcus Streptococcus gallolyticus Streptococcus equinus Streptococcus sanguinis Lactobacillales Aerococcus viridans Aerococcus Aerococcus christensenii Weissella paramesenteroides Lactobacillus plantarum Bacilli Pediococcus acidilactici Lactobacillus vaginalis Lactobacillus coleohominis Lactobacillus fermentum Lactobacillaceae Lactobacillus gasseri Lactobacillus Lactobacillus iners Lactobacillus jensenii Lactobacillus kalixensis Lactobacillus crispatus Lactobacillus crispatus Gemella haemolysans Staphylococcus aureus Staphylococcus epidermidis Bacillales Staphylococcus capitis Staphylococcus Staphylococcus lugdunensis Staphylococcus haemolyticus Staphylococcus hominis Staphylococcus warneri Fusobacteriaceae [Leptotrichia] amnionii Sneathia Sneathia sanguinegens Fusobacterium gonidiaformans Fusobacterium periodonticum Fusobacterium Fusobacterium periodonticum Fusobacterium nucleatum Fusobacterium periodonticum Asticcacaulis excentricus Agrobacterium tumefaciens Enhydrobacter aerosaccus Rhodopseudomonas palustris Alphaproteobacteria Asticcacaulis excentricus Neisseria subflava Neisseria Neisseria gonorrhoeae Neisseria subflava subflava Neisseria Methylotenera versatilis Burkholderia cepacia Parasutterella excrementihominis Sutterella stercoricanis Sutterella morbirenis Sutterellaceae Sutterella Sutterella wadsworthensis Rhizobacter dauci Pelomonas aquatica Comamonadaceae Delftia tsuruhatensis Escherichia coli Proteobacteria Enterobacteriaceae Raoultella planticola Serratia marcescens Haemophilus Haemophilusparainfluenzae parainfluenzae Terrahaemophilus aromaticivorans Haemophilus parainfluenzae Haemophilus parainfluenzae Pasteurellaceae Mannheimia granulomatis Haemophilus pittmaniae Psychrobacter pulmonis Gammaproteobacteria Moraxellaceae Pseudomonadales delta/epsilon subdivisions Acinetobacter baumannii Acinetobacter calcoaceticus/baumannii complex Acinetobacter calcoaceticus Pseudomonas fluorescens Pseudomonas aeruginosa Pseudomonas stutzeri Pseudomonas Pseudomonas fulvastutzeri Pseudomonas oryzihabitans Pseudomonas Pseudomonas fulva Pseudomonas plecoglossicida Pseudomonas plecoglossicida Pseudomonas putida group Pseudomonas monteilii Pseudomonas putida Pseudomonas mosselii Campylobacter ureolyticus Bilophila wadsworthia Alistipes finegoldii Porphyromonas Porphyromonas sp. type 1 Porphyromonas somerae Porphyromonas bennonis Porphyromonas endodontalis Porphyromonas asaccharolytica Porphyromonas uenonis Porphyromonas asaccharolytica Porphyromonas asaccharolytica Bacteroides nordii Bacteroides faecis Bacteroides Bacteroides xylanisolvens Bacteroides nordii Prevotella genogroup 5 Prevotella buccalis Prevotella genogroup 3 Prevotella buccalis Prevotella timonensis Prevotella genogroup 6 Prevotella genogroup 4 Prevotella genogroup 4 Prevotella genogroup 7 Prevotella genogroup 4 Prevotella genogroup 4 Prevotella bergensis Prevotella corporis Bacteroidales Prevotella Prevotella melaninogenica Prevotella disiens Prevotella intermedia Prevotella bivia Prevotella amnii Bacteroides uniformis Bacteroides Bacteroides stercoris Parabacteroides merdae candidate division TM7 genomosp. P1 candidate division TM7Division TM7 vaginal Candidate Slackia exigua Eggerthella sp. type 1 Coriobacteriaceae Atopobium Atopobium rimae Atopobium minutum Atopobium vaginae Mycobacterium novocastrense Corynebacterium ulceribovis Corynebacterium ureicelerivorans Corynebacterium pyruviciproducens Corynebacterineae Corynebacterium Corynebacterium accolens Corynebacterium tuberculostearicum Alloscardovia omnicolens Bifidobacteriaceae Actinobacteria (class) Gardnerella vaginalis Actinobacteridae Brevibacterium massiliense Brevibacterium Brevibacterium otitidis Brevibacterium paucivorans Dermacoccus nishinomiyaensis Actinomyces urogenitalis Actinomyces hongkongensis Actinomyces neuii Varibaculum cambriense Mobiluncus curtisii Mobiluncus Mobiluncus mulieris Actinomyces Actinomyces meyeri Actinomyces lingnae Arcanobacterium hippocoleae Arcanobacterium phocae Arcanobacterium Arcanobacterium haemolyticum Actinomycetaceae 0.1 Bifidobacterium breve Bifidobacterium Bifidobacterium bifidum Actinobaculum massiliense Dialister propionicifaciens Supplementary Figure 3B Dialister sp. type 2 Dialister Dialisterpropionicifaciens propionicifaciens Dialister propionicifaciens Dialister propionicifaciens propionicifaciens Dialister Dialister succinatiphilus Dialister pneumosintes Dialister Dialister micraerophilus Veillonellaceae Megasphaera micronuciformis MegasphaeraMegasphaera sp. type 2 Megasphaera sp. type 1 Firmicutes Veillonella montpellierensis VeillonellaVeillonella Veillonella atypica atypica Veillonella parvula Veillonella atypica BVAB2 BVAB3 Fastidiosipila sanguinis Faecalibacterium prausnitzii Bacteroides galacturonicusEubacterium siraeum Eubacterium eligens Dorea longicatena Moryella indoligenes Ruminococcus obeum Clostridiales Eubacterium rectale Roseburia faecis Roseburia hominis Roseburia intestinalis Roseburia inulinivorans Clostridiales Roseburia BVAB1 Eubacterium ramulusShuttleworthia satelles Catonella morbi Howardella ureilytica Candidatus Peptoniphilus massiliensis Bacteroides coagulans Peptoniphilus asaccharolyticus Peptoniphilus indolicus Peptoniphilus duerdenii Peptoniphilus Peptoniphilus harei Peptoniphilus lacrimalis Parvimonas micra Clostridiales Family XI. Incertae Sedis Finegoldia magna Anaerococcus hydrogenalis Anaerococcus vaginalis AnaerococcusAnaerococcus octavius Anaerococcus lactolyticus murdochii Anaerococcus Anaerococcus tetradius Anaerococcus prevotii Eubacterium saphenum Clostridium colicanis Peptostreptococcus anaerobius Peptostreptococcus Peptostreptococcus stomatis Mycoplasma hominis Clostridiales Ureaplasma parvum Ureaplasma Ureaplasma urealyticum Ureaplasma parvum parvum Ureaplasma Ureaplasma parvum Mycoplasma genitalium Mycoplasmataceae Enterococcus faecium Enterococcus durans Enterococcus durans Enterococcus Enterococcus avium Enterococcus faecalis Streptococcus parasanguinis Streptococcus agalactiae Streptococcus oralis Streptococcus mitis Streptococcus Streptococcusintermedius intermedius Streptococcus intermedius Streptococcus constellatus Streptococcus anginosus group Streptococcus intermedius Streptococcus intermedius Streptococcus anginosus Streptococcus Streptococcus mutans Streptococcus salivarius Streptococcus thermophilus Streptococcus salivarius salivarius Streptococcus Streptococcus gallolyticus Streptococcus equinus Streptococcus sanguinis Lactobacillales Aerococcus viridans Aerococcus Aerococcus christensenii Weissella paramesenteroides Lactobacillus plantarum Bacilli Pediococcus acidilactici Lactobacillus vaginalis Lactobacillus coleohominis Lactobacillus fermentum Lactobacillaceae Lactobacillus gasseri Lactobacillus Lactobacillus iners Lactobacillus jensenii Lactobacillus kalixensis Lactobacillus crispatus Lactobacillus crispatus Gemella haemolysans Staphylococcus aureus Staphylococcus epidermidis Bacillales Staphylococcus capitis Staphylococcus Staphylococcus lugdunensis Staphylococcus haemolyticus Staphylococcus hominis Staphylococcus warneri Fusobacteriaceae [Leptotrichia] amnionii Sneathia Sneathia sanguinegens Fusobacterium gonidiaformans Fusobacterium periodonticum Fusobacterium Fusobacterium periodonticum Fusobacterium nucleatum Fusobacterium periodonticum Asticcacaulis excentricus Agrobacterium tumefaciens Enhydrobacter aerosaccus Rhodopseudomonas palustris Alphaproteobacteria Asticcacaulis excentricus Neisseria subflava Neisseria Neisseria gonorrhoeae Neisseria subflava subflava Neisseria Methylotenera versatilis Burkholderia cepacia Parasutterella excrementihominis Sutterella stercoricanis Sutterella morbirenis Sutterellaceae Sutterella Sutterella wadsworthensis Rhizobacter dauci Pelomonas aquatica Comamonadaceae Delftia tsuruhatensis Escherichia coli Proteobacteria Enterobacteriaceae Raoultella planticola Serratia marcescens Haemophilus Haemophilusparainfluenzae parainfluenzae Terrahaemophilus aromaticivorans Haemophilus parainfluenzae Haemophilus parainfluenzae Pasteurellaceae Mannheimia granulomatis Haemophilus pittmaniae Psychrobacter pulmonis Gammaproteobacteria Moraxellaceae Pseudomonadales delta/epsilon subdivisions Acinetobacter baumannii Acinetobacter calcoaceticus/baumannii complex Acinetobacter calcoaceticus Pseudomonas fluorescens Pseudomonas aeruginosa Pseudomonas stutzeri Pseudomonas Pseudomonas fulvastutzeri Pseudomonas oryzihabitans Pseudomonas Pseudomonas fulva Pseudomonas plecoglossicida Pseudomonas plecoglossicida Pseudomonas putida group Pseudomonas monteilii Pseudomonas putida Pseudomonas mosselii Campylobacter ureolyticus Bilophila wadsworthia Alistipes finegoldii Porphyromonas Porphyromonas sp. type 1 Porphyromonas somerae Porphyromonas bennonis Porphyromonas endodontalis Porphyromonas asaccharolytica Porphyromonas uenonis Porphyromonas asaccharolytica Porphyromonas asaccharolytica Bacteroides nordii Bacteroides faecis Bacteroides Bacteroides xylanisolvens Bacteroides nordii Prevotella genogroup 5 Prevotella buccalis Prevotella genogroup 3 Prevotella buccalis Prevotella timonensis Prevotella genogroup 6 Prevotella genogroup 4 Prevotella genogroup 4 Prevotella genogroup 7 Prevotella genogroup 4 Prevotella genogroup 4 Prevotella bergensis Prevotella corporis Bacteroidales Prevotella Prevotella melaninogenica Prevotella disiens Prevotella intermedia Prevotella bivia Prevotella amnii Bacteroides uniformis Bacteroides Bacteroides stercoris Parabacteroides merdae candidate division TM7 genomosp. P1 candidate division TM7Division TM7 vaginal Candidate Slackia exigua Eggerthella sp. type 1 Coriobacteriaceae Atopobium Atopobium rimae Atopobium minutum Atopobium vaginae Mycobacterium novocastrense Corynebacterium ulceribovis Corynebacterium ureicelerivorans Corynebacterium pyruviciproducens Corynebacterineae Corynebacterium Corynebacterium accolens Corynebacterium tuberculostearicum Alloscardovia omnicolens Bifidobacteriaceae Actinobacteria (class) Gardnerella vaginalis Actinobacteridae Brevibacterium massiliense Brevibacterium Brevibacterium otitidis Brevibacterium paucivorans Dermacoccus nishinomiyaensis Actinomyces urogenitalis Actinomyces hongkongensis Actinomyces neuii Varibaculum cambriense Mobiluncus curtisii Mobiluncus Mobiluncus mulieris Actinomyces Actinomyces meyeri Actinomyces lingnae Arcanobacterium hippocoleae Arcanobacterium phocae Arcanobacterium Arcanobacterium haemolyticum Actinomycetaceae 0.1 Bifidobacterium breve Bifidobacterium Bifidobacterium bifidum Actinobaculum massiliense
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