Taxonomy of Human Intestinal Gram-Positive Bacteria Focus on Anaerobes Belonging to the Phyla Firmicutes and Actinobacteria Tomohiko FUJISAWA* * Labor

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1 Taxonomy of Human Intestinal Gram-Positive Bacteria Focus on Anaerobes Belonging to the Phyla Firmicutes and Actinobacteria Tomohiko FUJISAWA* * Laboratory of Food Hygiene, Faculty of Applied Life Science, Nippon Veterinary and Life Science University Archaea Bacteria Archaea Bacteria Bacteria Firmicutes Bacteroidetes Actinobacteria Proteobacteria Bacteria Archaea Bacteria Firmicutes Actinobacteria Abstract Bacteria Archaea Firmicutes Bacteroidetes Actinobacteria Proteobacteria Bacteria Archaea Firmicutes Actinobacteria Key words Firmicutes Actinobacteria Bacteria Actinobacteria Firmicutes 1

2 Bacteria Firmicutes Actinobacteria Furmicutes Negativicutes Lactobacillus Enterococcus 2 Bifidobacterium Bacteria Bacteria Acidobacteria Actinobacteria Aquificae Armatimonadetes Bacteroidetes Caldiserica Chlamydiae Chlorobi Chloroflexi Chrysiogenetes Cyanobacteria D e f e r r i b a c t e r e s D e i n o c o c c u s - T h e r m u s Dictyoglomi Elusimicrobia Fibrobacteres Firmicutes Fusobacteria Gemmatimonadetes Ignavibacteriae Lentisphaerae Nitrospira Planctomycetes Proteobacteria Spirochaetes Synergistetes Tenericutes Thermodesulfobacteria Thermotogae Verrucomicrobia Actinobacteria Bacteroidetes Deinococcus-Thermus Firmicutes Fusobacteria Lentisphaerae Proteobacteria Spirochaetes Synergistetes Tenericutes Verrucomicrobia 5 Acidobacteria Actinobacteria Bacteroidetes Chlamydiae Chloroflexi Cyanobacteria Deferribacteres Deinococcus-Thermus Fibrobacteres Firmicutes Fusobacteria Gemmatimonadetes Lentisphaerae Planctomycetes Proteobacteria Spirochaetes Tenericutes Verrucomicrobia 6 Actinobacteria Firmicutes Firmicutes Actinobacteria Bacteria Actinobacteria Actinobacteria 7 Coriobacteriia Actinobacteria - Coriobacteriia Coriobacteriia Coriobacteriales Eggerthellales 8 Coriobacteriales Coriobacteriaceae Atopobiaceae Coriobacteiaceae Eubacterium Collinsella Collinsella aerofaciens 9 Collinsella Collinsella aerofaciens 9 Collinsella intestinalis 10 Collinsella stercoris 10 Collinsella tanakaei 11 1 Atopobiaceae Atopobium Lactobacillus rimae Lactobacillus minutus Streptococcus parvulus Peptostreptococcus parvulus 12 Olsenella Lactobacillus uli Olsenella uli 13 Eggerthellales Eggerthellaceae Slackia Eubacterium exiguum Peptostreptococcus heliotrinreducens Slackia exigua Slackia heliotrinireducens 14 Slackia equolifaciens 15

3 Actinobacteria Coriobacteriia Coriobacteriales Coriobacteriaceae Collinsella Enorma Senegalimassilia Atopobiaceae Atopobium Olsenella Eggerthellales Eggerthellaceae Eggerthella Adlercreutzia Asaccharobacter Cryptobacterium Gordonibacter Paraeggerthella Slackia Actinobacteria Actinomycetales Actinomycetaceae Actinomyces Arcanobacterium Mobiluncus Trueperella Varibaculum Bifidobacteriales Bifidobacteriaceae Bifidobacterium Scardovia Corynebacteriales Corynebacteriaceae Corynebacterium Dietziaceae Dietzia Mycobacteriaceae Mycobacteium Nocardiaceae Gordonia Rhodococcus Micrococcales Micrococcaceae Micrococcus Arthrobacter Kocuria Rothia Bogoriellaceae Georgenia Brevibacteriaceae Brevibacterium Cellulomonadaceae Cellulomonas Tropheryma Dermabacteraceae Dermabacter Brachybacterium Dermacoccaceae Dermacoccus Kytococcus Intrasporangiaceae Janibacter Microbacteriaceae Microbacterium Agrococcus Curtobacterium Yonghaparkia Promicromonosporaceae Promicromonospora Cellulosimicrobium Micromonosporales Micromonosporaceae Micromonospora Propionibacteriales Propionibacteriaceae Propionibacterium Nocardioidaceae Aeromicrobium Streptomycetales Streptomycetaceae Streptomyces

4 Collinsella, Atopobium Slackia Collinsella intestinalis Collinsella stercoris Collinsella aerofaciens Collinsella tanakaei Atopobium rimae Atopobium parvulum Atopobium minutum Slackia equolifaciens Slackia piriformis Slacki exigua Slackia isoflavoniconvertens Slackia isoflavoniconvertens 16 Slackia Collinsella Atopobium Slackia - Bacilli Bacilli Bacillales Lactobacillales Bacillales Bacillus Staphylococcus Lactobacillales Enterococcaceae Enterococcus Lactobacillaceae Lactobacillus Streptococcaceae Streptococcus Aerococcaceae Carnobacteriaceae Leuconostocaceae Lactobacillaceae Enterococcaceae 2 - Actinobacteria Actinobacteria Actinobacteria Bifidobacteriales Bifidobacteriaceae Bifidobacterium Corynebactrium Micrococcus Actinobacteria Bacteria Firmicutes Firmicutes 5 Firmicutes Bacilli Clostridia Erysipelotrichia Negativicutes Thermolithobacteria Bacilli Clostridia Erysipelotrichia Negativicutes Firmicutes Lactobacilus Clostridium perfringens - Clostridia Clostridia Clostridiales Halanaerobiales Clostridiales Clostridiales Eubacteriaceae Peptostreptococcaceae Ruminococcaceae Lachnospiraceae 17 Clostridiaceae Clostridium Clostridium 18 Clostrisium Clostridium Eubacterium Peptostreptococcus 19Clostridium barkeri Eubacterium 19

5 Clostridium limosum 20 Eubacterium Eubacterium moniliforme Eubacterium tarantellae Sarcia Sarcina maxima Sarcina ventriculi Clostridium 20 Clostridium Clostridium butyricum Clostridium Clostridiales Mogibacterium Eubacterium timidum Mogibacterium timidum Mogibacterium pumilum Mogibacterium vescum 21 Mogibacterium Lachnospiraceae Roseburia 22 Lachnospiraceae Dorea Eubacterium formicigenerans 23 Dorea formicigenerans Dorea longicatena Eubacterium Eubacteriaceae 24 Eubacterium Eubacterium Eubacterium Actinobacteria Slackia Eubacterium Eubacterium aerofaciens Collinsella 9 Eubacterium rectale Agathobacter 25 Eubacterium lentum Eggerthella lenta 14 Eubacterium biforme Holdemanella biformis 26 Eubacterium cylindroides Faecalitalea cylindroides 26 Eubacterium fossor Atopobium fossor 27 Eubacterium lentum Eubacterium fossor Eubacterium Eubacterium Eubacterium Eubacterium Ruminococaceae Peptodstreptococcaceae Peptostreptococcus Lachnospiraceae Coprococcus 28 Coprococcus Coprococcus Peptostreptococcus 29 Peptostreptococcus Blautia 30 Peptostreptococcus Peptostreptococcus asaccharolyticus Peptostreptococcus harei Peptostreptococcus indolicus Peptostreptococcus ivorii Peptostreeptococcus lacrimalis Peptoniphilus 31 Peptostreptococcus hydrogenalis Peptostreptococcus l a c t o l y t i c u s P e p t o s t r e p t o c o c c u s o c t a v i u s Peptostreptococcus prevotii Peptostreptococcus tetradius Peptostreptococcus vaginalis Anaerococcus 31 Peptostreptococcus Peptostreptococcus anaerobius Peptostreptococcus russellii Peptostreptococcus canis Peptostreptococcus stomatis Peptostreptococcus parvulus Actinobacteria Atopobium Apotobium parvulum 12 32

6 Firmicutes Bacilli Bacillales Alicyclobacillaceae Tumebacillus Bacillaceae Aeribacillus Bacillus Geobacillus Lysinibacillus Oceanobacillus Virgibacillus Listeriaceae Brochothrix Paenibacillaceae Aneurinibacillus Brevibacillus Paenibacillus Planococcaceae Kurthia Planococcus Planomicrobium Sporosarcina Ureibacillus Staphylococcaceae Staphylococcus Bacillales Exiguobacterium Gemella Lactobacillales Aerococcaceae Abiotrophia Aerococcus Facklamia Carnobacteriaceae Granulicatella Enterococcaceae Enterococcus Tetragenococcus Lactobacillaceae Lactobacillus Pediococcus Leuconostocaceae Leuconostoc Weissella Streptococcaceae Lactococcus Streptococcus Clostridia Clostridiales Clostridiaceae Anoxynatronum Clostridium Hungatella Lactonifactor Paraclostridium Eubacteriaceae Anaerofustis Eubacterium Pseudoramibacter Lachnospiraceae Agathobacter Anaerostipes Blautia Butyrivibrio Cellulosilyticum Coprococcus Dorea Fusicatenibacter Hespellia Lachnoanaerobaculum Lachnobacterium Lachnospira Marvinbryantia Moryella Oribacterium Parasporobacterium Robinsoniella

7 Firmicutes Roseburia Oscillospiraceae Oscillibacter Peptococcaceae Peptococcus Desulfitobacterium Peptostreptococcaceae Asaccharospora Filifactor Intestinibacter Peptopstreptococcus Romboutsia Terrisporobacter Ruminococcaceae Acetanaerobacterium Anaerofilum Anaerotruncus Butyricicoccus Faecalibacterium Hydrogenoanaerobacterium Papillibacter Subdoligranulum Peptoniphilaceae Peptoniphilus Anaerococcus Parvimonas Finegoldia Christensenellaceae Christensenella Clostririales Catabacter Flavonifractor Howardella Mogibacterium Pseudoflavonifractor Tissierella Halanaerobiales Halobacteroidaceae Halanaerobaculum Erysipelotrichia Erysipelotrichales Erysipelotrichaceae Bulleidia Catenibacterium Coprobacillus Faecalitalea Eggerthia Holdemanella Holdemania Kandleria Solobacterium Turicibacter Negativicutes Acidaminococcales Acidaminococcaceae Acidaminococcus Phascolarctobacterium Veillonellales Veillonellaceae Allisonella Dialister Megasphaera Negativicoccus Veillonella Selenomonadales Selenomonadaceae Megamonas Mitsuokella Selenomonas

8 Clostridium Clostridium acetobutylicum Clostridium aldenense Clostridium aminovalericum Clostridium asparagiforme Clostridium baratii Clostridium beijerinckii Clostridium bolteae Clostridium botulinum Clostridium butyricum Clostridium cadaveris Clostridium celatum Clostridium cellobioparum Clostridium chartatabidum Clostridium chauvoei Clostridium citroniae Clostridium clariflavum Clostridium clostridioforme Clostridium cochlearium Clostridium cocleatum Clostridium difficile Clostridium disporicum Clostridium fallax Clostridium felsineum Clostridium glycyrrhizinilyticum Clostridium herbivorans Clostridium hiranonis Clostridium hylemonae Clostridium indolis Clostridium innocuum Clostridium lactatifermentans Clostridium lavalense Clostridium leptum Clostridium malenominatum Clostridium methoxybenzovorans Clostridium methylpentosum Clostridium moniliforme Clostridium nexile Clostridium paraputrificum Clostridium perfringens Clostridium populeti Clostridium putrefaciens Clostridium ramosum Clostridium rectum Clostridium saccharogumia Clostridium saccharoperbutylacetonicum Clostridium sardiniense Clostridium sartagoforme Clostridium scindens Clostridium senegalense Clostridium septicum Clostridium sphenoides Clostridium spiroforme Clostridium sporogenes Clostridium sporoshaeroides Clostridium sticklandii Clostridium subterminale Clostridium symbiosum Clostridium tertium Clostridium tyrobutyricum Clostridium vincentii Clostridium viride Peptococcaceae Peptococcus Peptococcus niger Peptococcus Peptococcus niger Ruminococcaceae Faecalibacterium prausnitzii Fusobacterium 19 Fusobacterium 33 Blautia Clostridium coccoides productus hansenii hydrogenotrophicus luti shinkii Clostridium Blautia Clostridia Clostridiales Coprococcus Blautia Peptostreptococcus Peptoniphilus Anaerococcus - Erysipelotrichia Erysipelotrichia Erysipelotrichales Holdemanella Eubacterium biforme 26 Eggerthia Kandleria Lactobacillus catenaformis Lactobacillus vitulinus 34 - Negativicutes N e g a t i v i c u t e s S e l e n o m o n a d a l e s Acidaminococcaceae 35 Acidaminococcaceae Acidaminococcus Selenomonadales Veillonellales Megasphaera Megamonas Mitsuokella Selenomonas Veillonella Megamonas hypermegale 36 Mitsuokella multacida 36 Dialister pneumosintes 37 Bacteroides

9 Clostridium Clostridium barkei Eubacterium barkeri Clostridium bartlettii Intestinibacter bartlettii Clostridium bifermentans Paraclostridium bifermentans Clostridium bryantii Syntrophospora bryantii Syntrophomonas bryantii Clostridium coccoides Blautia coccoides Clostridium fervidum Caloramator fervidus Clostridium ghonii Paeniclostridium ghonii Clostridium glycolicum Terrisporobacter glycolicus Clostridium hathewayi Hungatella hathewayi Clostridium histolyticum Hathewaya histolytica Clostridium hydroxybenzoicum Sedimentibacter hydroxybenzoicus Clostridium irregulare Asaccharospora irregularis Clostridium lentocellum Cellulosilyticum lentocellum Clostridium limosum Hathewaya limosa Clostridium lituseburense Romboutsia lituseburensis Clostridium lortetii Sporohalobacter lortetii Clostridium mayombei Terrisporobacter mayombei Clostridium oxalicum Oxalophagus oxalicus Clostridium pfennigii Oxobacter pfennigii Clostridium proteoclasticum Butyrivibrio proteoclasticus Clostridium proteolyticum Hathewaya proteolytica Clostridium quercicolum Dendrosporobacter quercicolus Clostridium sordellii Paeniclostridium sordellii Clostridium thermaceticum Moorella thermoacetica Clostridium thermautotrophicum Moorella thermoautotrophica Clostridium thermocopriae Thermoanaerobacter thermocopriae Clostridium thermohydrosulfuricum Thermoanaerobacter thermohydrosulfuricus Clostridium thermosaccharolyticum Thermoanaerobacterium thermosaccharolyticum Clostridium thermosulfurigenes Thermoanaerobacterium thermosulfurigenes Clostridium villosum Filifactor villosus Eubacterium Eubacterium aerofaciens Collinsella aerofaciens Eubacterium alactolyticum Pseudoramibacter alactolyticus Eubacterium biforme Holdemanella biformis Eubacterium cylindroides Faecalitalea cylindroides Eubacterium exiguum Slackia exigua Eubacterium formicigenerans Dorea formicigenerans Eubacterium fossor Atopobium fossor Eubacterium hadrum Anaerostipes hadrus Eubacterium lentum Eggerthella lenta Eubacterium moniliforme Clostridium moniliforme Eubacterium plautii Flavonifractor plautii Eubacterium rectale Agathobacter rectalis Eubacterium saburreum Lachnoanaerobaculum saburreum Eubacterium suis Actinomyces suis Actinobaculum suis Eubacterium tarantellae Clostridium tarantellae Eubacterium timidum Mogibacterium timidum

10 Eubacterium Eubacterium barkeri Eubacterium brachy Eubacterium budayi Eubacterium callanderi Eubacterium cellulosolvens Eubacterium desmolans Eubacterium dolichum Eubacterium eligens Eubacterium hallii Eubacterium limosum Eubacterium multiforme Eubacterium nitritogenes Eubacterium ramulus Eubacterium ruminantium Eubacterium saphenum Eubacterium siraeum Eubacterium sulci Eubacterium tenue Eubacterium tortuosum Eubacterium ventriosum 1 Bacteroides Proteobacteria Gemmiger formicilis Firmicutes Firmicutes 38 Firmicutes Negativicutes Butyrivibrio Roseburia Archaea Archaea Crenarchaeota Euryarchaeota Korarchaeota Nanoarchaeota Thaumarchaeota Peptostreptococcus Peptostreptococcus asaccharolyticus Peptoniphilus asaccharolyticus Peptostreptococcus barnesae Gallicola barnesae Peptostreptococcus harei Peptoniphilus harei Peptostreptococcus heliotrinreducens Slackia heliotrinireducens Peptostreptococcus hydrogenalis Anaerococcus hydrogenalis Peptostreptococcus indolicus Peptoniphilus indolicus Peptostreptococcus ivorii Peptoniphilus ivorii Peptostreptococcus lacrimalis Peptoniphilus lacrimalis Peptostreptococcus lactolyticus Anaerococcus lactolyticus Peptostreptococcus magnus Finegoldia magna Peptostreptococcus micros Micromonas micros Parvimonas micra Peptostreptococcus octavius Anaerococcus octavius Peptostreptococcus parvulus Streptococcus parvulus Atopobium parvulum Peptostreptococcus prevotii Anaerococcus prevotii Peptostreptococcus productus productus Blautia producta Peptostreptococcus tetradius Anaerococcus tetradius Peptostreptococcus vaginalis Anaerooccus vaginalis hansenii Blautia hansenii hydrogenotrophicus Blautia hydrogenotrophica luti Blautia luti obeum Blautia obeum palustris Trichococcus palustris pasteurii Lactosphaera pasteurii Trichococcus pasteurii productus Blautia producta schinkii Blautia schinkii

11 Peptococcus Peptococcus asaccharolyticus Peptostreptococcus asaccharolyticus Peptoniphilus asaccharolyticus Peptococcus glycinophilus Peptostreptococcus micros Micromonas micros Parvimonas micra Peptococcus heliotrinreducens Peptostreptococcus heliotrinreducens Slackia heliotrinireducens Peptococcus indolicus Peptostreptococcus indolicus Peptoniphilus indolicus Peptococcus magnus Peptostreptococcus magnus Finegoldia magna Peptococcus prevotii Peptostreptococcus prevotii Anaerococcus prevotii Peptococcus saccharolyticus Staphylococcus saccharolyticus Coprococcus,, Blautia, Peptostreptococcus, Peptoniphilus Anaerococcus Coprococcus catus Coprococcus eutactus Coprococcus comes albus bromii gauvreauii lactaris torques faecis gnavus callidus flavefaciens champanellensis Blautia wexlerae Blautia luti Blautia faecis Blautia glucerasea Blautia coccoides Blautia producta Blautia hansenii Blautia stercoris Blautia hydrogenotrophica Blautia obeum Peptostreptococcus anaerobius Peptostreptococcus stomatis Peptoniphilus harei Peptoniphilus timonensis Peptoniphilus indolicus Peptoniphilus asaccharolyticus Peptoniphilus lacrimalis Anaerococcus prevotii Anaerococcus vaginalis Anaerococcus senegalensis Anaerococcus hydrogenalis Anaerococcus octavius Euryarchaeota Methanobacteria Methanobacteriales Methanobacteriaceae Methanobrevibacter smithii Methanobrevibacter ruminantium Methanosphaera stadtmanae Euryarchaeota Thermoplasmata Methanomassiliicoccales Methanomassiliicoccaceae Methanomassiliicoccus luminyensis 1 Bacteria Actinobacteria Firmicutes Firmicutes Lactobacillus Archaea Euryarchaeota Methanobacteria Methanobacteriales Methanobacteriaceae Methanobrevibacter ruminantium Methanobrevibacter smithii Methanosphaera stadtmanae Thermoplasmata Methanomassiliicoccales Methanomassiliicoccaceae Methanomassiliicoccus luminyensis Clostridium perfringens Actinobacteria Bifidobacterium

12 Firmicutes Actinobacteria Firmicutes Blautia coccoides Blautia producta Blautia obeum Megasphaera elsdenii Butyrivibrio crossotus Agathobacter rectalis Eubacterium ventriosum Clostridium indolis Clostridium perfringens Lactobacillus crispatus Mitsuokella multacida Actinobacteria Propionibacterium avidum Collinsella aerofaciens Atopobium parvulum Eggerthella lenta Firmicutes Actinobacteria Coriobacteriia Coriobacteriia Coriobacteriales Coriobacteriaceae Atopobiaceae Eggerthellales Eggerthellaceae 9 Eubacterium aerofaciens Collinsella Collinsella aerofaciens 10 Collinsella Collinsella stercoris Collinsella intestinalis

13 11 Slackia piriformis Collinsella tanakaei Coriobacteriaceae 12 Lactobacillus minutus Lactobacillus rimae Streptococus parvulus Atopobium 13 Coriobacteriaceae Olsenella Lactobacillus uli Olsenella uli Olsenella profusa 14 Coriobacteriaceae Eubacterium exiguum et al Peptostreptococcus heliotrinreducens Slackia exigua Slackia heliotrinireducens Eubacterium lentum Eggerthella lenta 15 Slackia equolifaciens Clostridium 19 Clostridium 20 Clostridium Clostridium butyricum 21 Mogibacterium pumilum Mogibacterium vescum Eubacterium timidum et al Mogibacterium tumidum 22 Roseburia cecicola 23 Eubacterium formicigenerans Dorea formicigenerans Dorea longicatena 24 Eubacterium 25 Eubacterium rectale et al Agathobacter Agathobacter rectalis Agathobacter ruminis 26 Faecalicoccus acidiformans Streptococcus pleomorphus et al Eubacterium biforme Eubacterium cylindroides et al Faecalicoccus pleomorphus Holdemanella biformis Faecalitalea cylindroides Erysipelotrichaceae 27 Eubacterium fossor Atopobium Atopobium fossor C l o s t r i d i u m c o c c o i d e s hansenii hydrogenotrophicus luti productus schinkii Blautia coccoides Blautia hansenii Blautia hydrogenotrophica Blautia luti Blautia producta Blautia schinkii Blautia wexlerae

14 31 Anaerococcus Peptoniphilus Gallicola Peptostreptococcus Fusobacterium prausnitzii Faecalibacterium prausnitzii 34 Lactobacillus catenaformis Lactobacillus vitulinus et al Eggerthia catenaformis Kandleria vitulina 35 Neagativicoccus succinicivorans Veillonellaceae Negativicutes Selenomonadales Acidaminococcaceae Firmicutes Oribacterium catoniae Catonella morbi Hallella seregens Johnsonella ignava Dialister pneumosintes