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Table 3 Genus and species catalogue

From: Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter

Genus

Species under the corresponding genus

Samples carrying these species

Blastocatella sp.

  

Actinomyces sp.*

  
 

A. odontolyticus

S13, S7, S8

 

A. graevenitzii

S7, S8, S14

 

A. oris

S8

Arcanobacterium sp.

  

Bifidobacterium sp.*

  
 

B. longum

S16, S9, S17, S15, S10

 

B. ramosum

S16, S15

 

B. secularae

S7

 

B. bifidum

S17

 

B. pullorum

S17

 

B. sp. MRM 8. 19

S2

 

B. aerophilum

S15

 

B. angulatum

S2, S9, S10, S15, S19, S17

 

B. animalis

S15, S10

 

B. avesanii

S15

 

B. biavatii

S15

 

B. sp. MC10

S15, S17

Corynebacterium sp.*

  
 

C. falsenii

S3

 

C. bovis

S16

 

C. accolens

S8, S10, S13, S14

 

C. kroppenstedtii

S9, S20, S10, S13

 

C. cystitidis

S20

 

C. sp. M72

S10

 

C. doosarense

S1

 

C. simulans

S14

 

C. sp. NML98-0116

S16

 

C. glaucum

S7

 

C. sp. 1938BRRJ

S7, S11, S13, S14

 

C. sp3210O2

S7, S8

 

C. sp. NML080024

S7

 

C. durum

S20

Turicells sp.

  
 

T. otidis

S1, S3, S4, S7, S14, S15, S20

Dietzia sp.

  

Rhodococcus sp.

  

Brevibacterium sp.

  
 

B. luteolum

S17

Kytococcus sp.

  

Candidatus Planktoluna sp.

  

Microbacterium sp.

  

Micrococcus sp.

  
 

M. terreus

S14

Rothia sp.

  
 

R. dentocariosa

S7, S8, S11, S2, S13, S14

 

R. aeria

S11

 

R. sp. HMSC065C03

S14

Friedmanniella sp.

  

Mamoricola sp.

  

Cutibacterium sp.

  

Streptomyces sp.

  
 

S. sp. Q1

S13, S14

Libanicoccus sp.

  
 

L. massiliensis

S18, S19, S9, S17, S12, S13

Enterorhabdus sp.

  

Slckia sp.

  
 

S. hellotrinireducens

S15, S17, S20, S12, S10, S13

Bacteroides sp.*

  
 

B. plebius

S7, S10,

 

B. fragilis

S15, S19

 

B. propionicifaciens

S10, S15

 

B. sp. CAG:1060_57_27

S5

 

B. vulgatus

S10, S13

 

B. acidifaciens

S13

 

B. paurosaccharolyticus

S13

Butyricimonas sp.

  

Odoribacter sp.

  

Porphyromonas sp.

  
 

P. sp. oral taxon 278 K

S3

Alloprevotella sp.*

  
 

A. tannerae

S15, S20

 

A. rava

S2, S5, S19, S13

Prevotella sp.

  
 

p. enoeca

S6, S11

 

P. micans

S8

 

P. sp. AN5135

S15, S2

 

P. copri

S19, S12, S2, S5, S13

 

P. sp. oral clone ASCG10

S19, S12

 

P. sp. HJM029

S12

 

P. sp. 310-5

S13

 

P. marshii

S18, S7, S15, S19, S12, S2

 

P. nigrescens

S8, S20, S11

 

P. stercorea

S15, S19, S12, S5

 

P. sp. 152R-1a

S19

 

P. intermedia

S2

 

P. sp. HUN102

S2

 

P. sp. oral cloneKWO35

S2

Parabacteroides sp.

  

Flectobacillus sp.

  

Bergeyella sp.

  
 

B. sp. AF14

S8

Capnocytophaga sp.

  
 

C. sputigena

S8

 

C. ochracea

S11

 

C. sp. oral clone ID062-W

S2

Chryseobacterium sp.

  

Deinococcus sp.

  
 

D. geothermalis

S6

Exiguobacterterium sp.

  

Gemelia sp.

  
 

G. sanguinis

S3, S8, S2, S14

 

G. morbillorum

S8, S20

Effusibacillus sp.

  

Bacillus sp.

  

Planococcus sp.

  

Staphylococcus sp.

  
 

S. haemolyticus

S14

 

S. simulans

S14

Aerococcus sp.

  
 

A. vaginalis

S13, S20

Dolosigranulum sp.

  

Granulicatella sp.

  
 

G. sp. BB-11

S8, S20, S11, S14

 

G. sp. canine oral taxon O95

S14

Enterococcus sp.

  
 

E. faecium

S16

 

E. italicus

S11, S14

 

E. xinjiangensis

S16

 

E. casseliflavus

S10

 

E. hermanniensis

S10

 

E. durans

S10

Lactobacillus sp.*

  
 

L. coryniformis

S11

 

L. satsumensis

S14

Lactococcus sp.

  

Streptococcus sp.*

  
 

S. agalactiae

S2, S6, S3, S7, S8, S11, S10, S14

 

S. pneumoniae

S8, S17, S11, S2, S10, S1, S14

 

S. parasanguinis

S2, S5, S6, S3, S7, S8, S11, S10, S13, S14, S17, S20

 

S. anginosus

S18, S3, S4, S7, S8, S17, S20, S2, S10, S13, S14

 

S. dannielliae

S18, S3, S4, S16, S20, S11, S12, S2, S10

 

S. ferus

S18

 

S. pantholopis

S3

 

S. sp. oral clone ASCB12

S3, S7, S8, S17, S20, S11, S10, S14

 

S. sp. oral taxon GS9

S3, S11, S14

 

S. didelphis

S16

 

S. equinus

S4

 

S. parasuis

S16

 

S. sanguinis

S7, S8, S17, S14

 

S. sp. DD04(2016)

S7, S11, S14

 

S. sinensis

S7

 

S. sp. XJ149-N32

S7, S8, S11, S2, S14

 

S. vestibularis

S7, S8, S17, S11

 

S. mutans

S20

 

S. cristatus

S8, S20, S14

 

S. equi

S10, S14

 

S. gordonii

S14

 

S. mitis

S14

Clostridium sp.*

  
 

C. magnum

S1, S2, S3, S4, S15, S17, S18, S19, S20

 

C. sp. Marseille

S15, S19, S19, S12

 

C. sp. CE6

S19, S5, S10, S13

 

C. sp. CAG:288

S12

 

C. sp. Culture-Jar-56

S5

Lutispora sp.

  

Fusibacter sp.

  

Mogibacterium sp.

  

Alkalibacter sp.

  

Agathobacter sp.

  

Anaerosporobacter sp.

  

Anaerostipes sp.

  

Blautia sp.*

  
 

B. massiliensis

S18, S19, S9, S20, S2, S5, S10, S13

 

B. hydrogenotrophica

S10, S13

 

B. stercosis

S13

Catonella sp.

  

Dorea sp.

  
 

D. formicigenerans

S7, S19, S9, S17, S20, S12, S5, S10

 

D. longicatena

S2, S19

Lachnoclostridium sp.

  
 

[Clostridium]polysaccharolyticum

S15

Roseburia sp.

  
 

R. hominis

S6, S17, S2, S5

 

R. sp. 1120

S9, S10

Shuttleworthia sp.

  

Stomatobaculum sp.

  

Oscilibacter sp.

  

Desulfotomaculum sp.

  

Peptostreptococcus sp.*

  

Faecalibacterium sp.*

  
 

F. prausnitzii

S2, S12, S18, S19, S20

Fastidiosipila sp.

  

Ruminiclostridium sp.

  
 

Eubacterium siraeum

S18, S19, S20, S12, S13

 

Clostridium leptum

S19, S20, S12, S5

Ruminococcus sp.

  
 

R. sp. CE2

S16, S15, S19, S2, S10, S13

 

R. sp. YE58

S15, S9, S10

 

R. sp. RLB3

S9, S12

 

R. sp. W22

S9, S17, S10, S13

 

R. sp. 653

S17

 

R. bromii

S12, S5

 

R. sp. YE281

S12

 

R. sp. ID1

S2

 

R. gauvreaucii

S5

 

R. sp. Marseille-P328

S13

Subdoligranulum sp.

  

Dethiobacter sp.

  

Catenibacterium sp.

  
 

C. mitsuokai

S18, S7, S15, S19, S9, S5, S17

Holdemanella sp.*

  

Solobacterium sp.

  

Turicibacter sp.

  

Phascolarctobacterium sp.

  
 

P. sp. 377

S17

 

P. sp. canine oral taxon 212

S17, S5

Megamonas sp.

  

Dialister sp.*

  
 

D. sp. 67

S18, S8, S15, S19, S9, S17, S20, S12, S2, S10, S13

 

D. succinatiphilus

S17

Veillonella sp.

  
 

V. sp. oral clone OH1A

S3, S8, S20, S10, S13.S14

 

V. sp. oral taxon 780

S8, S2, S13

 

V. atypica

S17, S13

 

V. sp. 2011-11eoVSA-F2

S17

 

V. magna

S20

Anaerococcus sp.

  
 

A. sp. S138

S4

 

A. prevotii

S16

 

A. sp. S194

S16

 

A. octavius

S7

Peptoniphilus sp.

  

Fusobacterium sp.

  
 

F. nucleatum

S11

 

F. russii

S2

Leptotricha sp.

  
 

L. sp. oral clone FP036

S11

 

L. sp. oral taxon 212

S11, S2, S14

 

L. sp. oral taxon 847

S11, S2

 

L. buccalis

S14

Streptobacillus sp.

  
 

S. hongkonggensis

S6, S20

Brevundimonas sp.

  

Methylobacterium sp.*

  

Paracoccus sp.

  

Actererythrobacter sp.

  

Novosphingobium sp.

  

Sphingomonas sp.

  

Lautropia sp.

  
 

L. mirabilis

S2, S6, S11, S13, S14

Ralstonia sp.

  

Parasutterella sp.

  
 

P. excrementihominis

S10

Sutterella sp.

  
 

S. sp. YIT-12072

S7, S5

Neisseria sp.*

  
 

N. meningitidis

S18, S19, S20

 

N. shayeganii

S18, S19, S20

 

N. elongata

S11, S14

 

N. flavescens

S11

 

N. lactamica

S2

Simonsiella sp.

  

Campylobacter sp.

  
 

C. faecalis

S18

 

C. concisus

S11

Helicobacter sp.

  
 

H. pylori

S2, S6, S7, S11, S14,

Shewanella sp.

  

Rheinheimera sp.

  

Buttiauxella sp.

  

Candidatus Benitsuchiphilus sp.

  

Candidatus Blochmannia sp.

  

Citrobacter sp.

  
 

C. amalonaticus

S10

Eschericia sp.

  
 

E. coli

S1, S2, S3, S4, S6, S8, S10, S11, S13, 16, S17, S19, S20

 

E. albertii

S1, S2, S4, S6, S10, S11, S13, S20

 

E. sp.

S1, S11

Klebsiella sp.

  
 

K. sp. A4

S1, S2, S6, S13, S18

 

K. pneumoniae

S4, S7, S10

 

K. aerogenes

S7

Shigella sp.

  
 

S. dysenteriae

S6, S11

 

S. sonnei

S6, S10, S16

Shimwella sp.

  

Xenorhabdus sp.

  

Brenneria sp.

  
 

B. sp. DAF NE_Bnig-1

S4

 

B. populi

S10

Dickeya

  

Serratia sp

  
 

S. marcescens

S3, S11

Alcanivorax sp.

  

Halomonas sp.

  

Aggregatibacter sp.

  

Haemophilus sp.

  
 

H. haemolyticus

S4, S6, S8

 

H. parainfluenzae

S4, S8, S14

 

H. pittmaniae

S8

 

H. sp. oral clone BJ021

S17

 

H. sputorum

S11, S17

 

H. influenzae

S1

Acinetobacter sp.*

  
 

A. baumanii

S19

 

A. sp.

S19

 

A. calcoaceticus

S12

Moraxella sp.

  
 

M. osloensis

S6, S7

Pseudomonas sp.

  
 

P. putida

S1

Vibrio sp.*

  
 

V. cholerae

S1, S2, S5, S6, S8, S9, S11, S12, S15, S17, S18, S19, S20

 

V. metoecus

S18, S13, S14

 

V. neptunius

S18

 

V. proteolyticus

S18

 

V. parahaemolyticus

S13

 

V. sp. NJ-2

S13

Treponema sp.

  
 

T. pectinovorum

S20

 

T. berlinense

S5

Fretibacterium sp.

  

Mycoplasma

  
 

M. muris

S10

Akkermansia sp.*

  
 

A. muciniphila

S5, S6, S7, S8, S13, S15, S16, S18, S19, S20

 

A. glycaniphila

S5

Mobiluncus sp.

  

Gardnerella sp.

  

Mycobacterium sp.

  

Brachybacterium sp.

  

Serinicoccus sp.

  

Glutamibacter sp.

  

Kocuria sp.

  

Nesterenkonia sp.

  

Propioniciclava sp.

  
 

P. sp. SCSIO_13291

S18

Atopobium sp.

  

Olsenella sp.

  

Collinsella sp.

  
 

C. aerofaciens

S18, S4, S16, S8, S15, S19, S9, S17, S20, S11, S12, S2, S5, S10, S1

 

C. bouchesdurhonensis

S15, S18, S19, S9, S17, S20, S12, S14

 

C. ihuae

S18, S15, S19, S9, S17, S20, S12, S14

 

C. sp. Marseille-P3740

S15, S9, S17, S20

 

C. phocaeensis

S17

Senegalimassilea sp.

  

Gaiella sp.

  

Paludibacter sp.

  
 

P. jiangxiensis

S11, S16, S18

Macellibacteroides sp.

  

Massiiprevotella sp.

  
 

M. massiliensis

S1, S2, S5, S9, S12, S18, S19, S20

Prevotellamassilia sp

  
 

P. timonensis

S18, S19, S17, S20, S12, S2, S10

Alistipes sp.

  
 

A. finegoldii

S15

Empedobacter sp.

  

Arcticibacter sp.

  

Sphingobacterium sp.

  
 

S. sp. JAS3

S19, S20

Microcystis sp.

  
 

M. sp. SAG43. 90

S18

Elusimicrobium sp.

  
 

E. minutum

S12

Fibrobacter sp.

  

Lactobacillalis bacterium HY-36-1)

  

Weissella sp.

  

Howardella sp.

  
 

H. ureilytica

S2

Intestimonas sp.

  

Christensenella sp.

  
 

C. massiliensis

S5, S19

Butyricoccus sp.

  
 

B. faecihominis

S9, S17, S20, S13

Oxobacter sp.

  

Acidaminobacter sp.

  

Anaerofustis sp.

  

Eubacterium sp.

  
 

E. coprostanoligenes

S18, S19, S20

 

E. eligens

S2, S5, S10, S12, S17, S18, S19, S20

 

E. sp. oral clone DO 016

S3, S7, S8

 

E. sp. oral clone FX028

S7, S14

 

E. pyruvativorans

S12

 

E. sp. oral clone El074

S14

Butyrivibrio

  
 

B. crossotus

S12, S18, S19, S20

Eisenbergiella sp.

  

Fusicatenibacter sp.

  

Lachnospira sp.

  

Marvinbryantia sp.

  
 

M. formatexigens

S20, S13

Moryella sp.

  

Oribacterium sp.

  

Tyzzerella sp.

  

Peptococcus sp.

  

Romboutsia sp.

  

Candidatus soleaferrea

  

Fournierella sp.

  

Negativibacillus sp.

  

Papillibacter sp.

  

Phocea sp.

  

Saccharofermentans sp.

  
 

S. acetigenes

S20

Sporobacter sp.

  

Dielma sp.

  

Erysipelothrix sp.

  
 

E. larvae

S7

Anaerovibrio sp.

  

Mitsuokella sp.

  

Selemonas sp.

  
 

S. sputigena

S20

 

S. noxia

S11

Sporomusa sp.

  

Allisonella sp.

  
 

A. histaminiformans

S19, S9, S17, S12, S2

Megasphaera sp.

  
 

M. micronuciformis

S13

Finegoldia sp.

  

Parvimonas sp.

  

Cetobacterium sp.

  

Craurococcus sp.

  

Roseomonas sp.

  

Candidatus Alysiosphaera

  

Sphaerotilus sp.

  
 

S. natans

S9

Comamonas sp.

  
 

C. aquatica

S12

 

C. testosteroni

S12

Diaphorobacter sp.

  

Oxalobacter sp.

  
 

O. formigenes

S18, S19, S10

Eikenella sp.

  

Kingella sp.

  
 

K. genomosp. P1 oral clone MB2_C20

S11

Thiobacillus sp.

  

Azonexus sp.

  

Zoogloea sp.

  

Desulfomicrobium sp.

  
 

D. baculatum

S18, S3, S4, S15, S19, S17, S20, S2, S5, S1, S14

Bilophila sp.

  

Desulfovibrio sp.

  
 

D. putealis

S3, S4, S15, S17, S2, S1, S14

 

D. sp. enrichment clone JdgSrb011

S11

Mailhella sp.

  
 

M. massiliensis

S18, S19, S20, S12

Pelobacter sp.

  

Geobacter sp.

  

Arcobacter sp.

  

Sulfurospirillum sp.

  
 

S. deleyianum

S2, S17, S20

Aeromonas sp.

  

Anaerobiospirillum sp.

  

Ruminobacter sp.

  

Succinivibrio sp

  
 

S. dextrinosolvens

S18, S19

Plesiomonas sp.

  

Cronobacter sp.

  

Buchnera sp.

  
 

B. aphidicola

S18

Edwardsiella sp.

  

Morganella sp.

  

Methyloparacoccus sp.

  

Actinobacillus sp.

  

Aliivibrio sp.

  

Lysobacter sp.

  

Stenotrophomonas sp.

  

Bacteriovorax sp.

  

Peredibacter sp.

  

Brachyspira sp.

  

Asteroleplasma sp.

  

Gordonia sp.

  

Tessaracoccus sp.

  

Candidatus Saccharimonas

  

Listeria sp.

  
 

L. floridensis

S16

Abiotrophia sp.

  
 

A. defectiva

S1, S2, S3, S8, S17, S20, S11, S13, S14

Facklamia sp.

  

Ignavigranum sp.

  

Melissococcus sp.

  

Pilibacter sp.

  

Leuconostoc sp.

  

Epulopiscium sp.

  

Anaerovorax sp.

  

Johnsonella sp.

  
 

J. ignava

S14

Clostridioides

  
 

C. difficile

S3, S8

Halanaerobium sp.

  

Anaeroglobus sp.

  

Murdochiella sp.

  

Ignavibacterium sp.

  

Magnetococcus sp.

  

Vogesella sp.

  

Marinobacter sp.

  

Franconibacter sp.

  
 

F. pulveris

S1, S3, S11

Pantoea sp.

  
 

P. agglomerans

S4

 

P. conspicua

S16

 

P. sp. R21

S14

Coxiella sp.

  

Ureaplasma sp.

  

Varibaculum sp.

  

Lawsonella sp.

  
 

L. clevelandensis

S7

Williamsia sp.

  

Arthrobacter sp.

  

Saccharopolyspora sp.

  

Flavobacterium sp.

  
 

F. caeni

S2

Moheibacter sp.

  

Alkaliphilus sp.

  
 

A. sp. LacT

S11

Acetobacterium sp.

  
 

A. woodii

S11

Desulfosporosinus sp.

  

Anaerotruncus sp.

  

Negativicoccus sp.

  

Fimbriiglobus sp.

  

Haliangium sp.

  

Enterobacter sp.

  
 

E. cloacae

S10

 

E. hormaechei

S1

Salmonella sp.

  
 

S. enterica

S11

Erwinia sp.

  
 

E. teleogrylli

S16

Proteus sp.

  
 

P. mirabilis

S14

Sodalis sp.

  

Hahella sp.

  
 

H. ganghwensis

S4

Phocoenobacter sp.

  

Perlucidibaca sp.

  

Luteimonas sp.

  

Arcella sp.

  
 

A. hemisphaerica

S1, S4

Bryobacter sp.

  

Aurantimicrobium sp.

  

Huakuichenia sp.

  

Propionimicrobium sp.

  

Emticicia sp.

  

Cloacibacterium sp.

  

Salinicoccus sp.

  

Proteiniclasticum sp.

  

Ethanoligenens sp.

  

Ezakiella sp.

  

Gallicola sp.

  

Helcococcus sp.

  
 

H. sueciensis

S7

Limnobacter sp.

  

Dechloromonas sp.

  

Propionivibrio sp.

  

Acidibacter sp.

  

Nocardia sp.

  

Pseudopropionibacterium sp.

  

Barnesiella sp.

  

Culturomica sp.

  

Hydrogenispora sp.

  

Atopococcus sp.

  

Catellicoccus sp.

  

Fenollaria sp.

  
 

F. timonensis

S7

Neofamilia sp.

  
 

N. massiliensis

S7

Sarcina sp.

  

Acetoanaerobium sp.

  

Bulleidia sp.

  
 

B. extructa

S8

Candidatus Stoquefichens

  

Coprobacillus sp.

  

Erysipelatoclostridium sp.

  

Sedimentibacter sp.

  

Aureimonas sp.

  

Aquabacterium sp.

  

Paraburkholderia sp.

  

Massilia sp.

  

Candidatus Babela

  

Cardiobacterium sp.

  

Legionella sp.

  

Bdellovibrio sp.

  
 

B. sp. SRP1

S9

Illumatobacter sp.

  

Acidothermus sp.

  

Haloactinopolyspora sp.

  

Quadrisphaera sp.

  

Georgenia sp.

  

Cellulomonas sp.

  

Dermabacter sp.

  

Pseudoclavibacter sp.

  

Nocardioides sp.

  
 

N. sp. N37

S15

Eggerthella sp.

  

Roultibacter sp.

  
 

R. timonensis

S8, S20

Rubrobacter sp.

  

Dysgonomonas sp.

  

Tannerella sp.

  
 

T. forsythia

S8, S2, S1

Asinibacterium sp.

  

Sediminibacterium sp.

  
 

S. sp. LT21-MRL

S8

Marinoscilum sp.

  

Neochlamydia sp.

  

Paenibacillus sp.

  

Eremococcus sp.

  

Lacticigenium sp.

  
 

L. naphtae

S8, S17, S20, S11, S10, S14

Tetragenococcus sp.

  

Vagococcus sp.

  

Lachnoanaerobaculum sp.

  

Filibacter sp.

  
 

F. alocis

S14

Eggerthia sp.

  
 

E. catenaformis

S8, S14

Hyphomicrobium sp.

  

Candidatus Ovatusbacter sp

  

Cellvibrio sp.

  

Yersinia sp.

  

Psychrobacter sp.

  

Pseudoxanthomonas sp.

  

Thermomonas sp.

  

Candidatus Ancillula sp.

  

Aeriscardovia sp.

  

Pseudoscardovia sp.

  

Candidatus Aquiluna sp.

  

Candidatus Limnoluna sp.

  

Haematomicrobium sp.

  

Nakamurella sp.

  

Dinghuibacter sp.

  

Pasteuria sp.

  

Alloiococcus sp.

  

Flavonifractor sp.

  
 

F. plautii

S15, S17

Caloranaerobacter sp.

  

Caminicella sp.

  

Syntrophococcus sp.

  

Coprothermobacter sp.

  

Singulisphaera sp.

  

Pirellula sp.

  

Plantoptrus sp.

  

Devosia sp.

  

Amaricoccus sp.

  

Reyranella sp.

  

Thiomonas sp.

  

Undibacterium sp.

  

Duodenibacillus sp.

  
 

D. massiliensis

S12

Desulfobulbus sp.

  

Pajaroellobacter sp.

  

Mariprofundus sp.

  

Luteolibacter sp.

  

Verrucomicrobium sp.

  

Holophaga sp.

  
 

H. foetida

S19

Acidimicrobium sp.

  

Cellulosimicrobium sp.

  

Rikenella sp.

  

Marinifilum sp.

  

Candidatus Latescibacter sp.

  

Trichococcus sp.

  

Colidextribacter sp.

  
 

C. massiliensis

S19, S20

Proteiniborus sp.

  

Caloramator sp.

  

Hungatella sp.

  

Acetitomaculum sp.

  
 

A. ruminis

S10, S14

Cellulosilyticum sp.

  

Herbinix sp.

  

Robinsoniella sp.

  

Sellimonas sp.

  

Peptoclostridium sp.

  

Acetivibrio sp.

  

Anaerofilum sp.

  

Hydrogenoanaerobacterium sp.

  

Oscillospira sp.

  

Catenisphaera sp.

  

Dubosiella sp.

  
 

D. newyorkensis

S19

Schwartzia sp.

  

Gottschalkia sp.

  

Victivallis sp.

  

Candidatus Paracaedibacter sp.

  

Enhydrobacter sp.

  

Komagataeibacter sp.

  

Ideonella sp.

  

Acidovorax sp.

  

Alicycliphilus sp.

  

Delftia sp.

  

Alysiella sp.

  

Vitreoscilla sp.

  
 

V. stercoraria

S5

Dechlorobacter sp.

  

Azoarcus sp.

  

Thauera sp.

  

Geothermobacter sp.

  

Succinatimonas sp.

  

Pseodoalteromonas sp.

  

Psychromonas sp.

  

Woeseia sp.

  

Candidatus Rosenkranzia

  

Marinomonas sp.

  

Alkanindiges sp.

  

Candidatus Parabeggiatoa sp.

  

Dokdonella sp.

  

Piscicoccus sp.

  

Agromyces sp.

  

Sanguibacter sp.

  

Sanguibacteroides sp.

  

Enorma sp.

  

Paraeggerthella sp.

  

Nubsella sp.

  

Pedobacter sp.

  
 

P. terricola

S9

Caldicoprobacter sp.

  

Lactonifactor sp.

  

Coprococcus sp.

  
 

C. catus

S9, S5

Pseudobutyrivibrio sp.

  
 

P. sp. CA38

S9

Faecalibaculum sp.

  

Faecalitalea sp.

  

Merdibacter sp.

  

Gemmatirosa sp.

  

Microvirga sp.

  

Candidatus Thiosymbion sp.

  

Oblitimonas sp.

  

Alloscardovia sp.

  

Leucobacter sp.

  

Longispora sp.

  

Acetatifactor sp.

  

Cryptanaerobacter sp.

  

Breznakia sp.

  

Succiniclasticum sp.

  

Sneathia sp.

  

Kaistia sp.

  
 

K. sp. TBD058

S17

Hellea sp.

  

Pseudoruegeria sp.

  
 

P. marunistellae

S17

Erythrobacter sp.

  

Candidatus Accumulibacter sp.

  

Rhodoferax sp.

  

Anaeromyxobacter sp.

  

Mannheimia sp.

  
 

M. haemolytica

S17

Mesocricetibacter sp.

  

Fluviicoccus sp.

  

Photobacterium sp.

  

Dermacoccus sp.

  

Dactylosporangium sp.

  

Propionibacterium sp.

  

Coriobacterium sp.

  

Cryptobacterium sp.

  

Gordonibacter sp.

  

Phocoeicola sp.

  

Rufibacter sp.

  

Truepera sp.

  

Desulfuribacillus sp.

  

Oceanobacillus sp.

  

Sporosarcina sp.

  

Marinilactibacillus sp.

  
 

M. sp. G13. 51

S13

Candidatus Arthromitus sp.

  

Guggenheimella sp.

  

Proteocatella sp.

  

Terrisporobacter sp.

  

Quinella sp.

  

Acidaminococcus sp.

  

Anaerospora sp.

  

Dethiosulfatibacter sp.

  

Tissierella sp.

  

Asticcacaulis sp.

  

Sphingobium sp.

  

tepidomonas sp.

  

Halioglobus sp.

  

Candidatus Stammerula sp.

  

Izhakiella sp.

  

Pectobacterium sp.

  

Aquicella sp.

  

Scardovia sp.

  
 

S. inopinata

S20

Luedemannella sp.

  

Rosemarinus sp.

  

Maritimimonas sp.

  

Bavariicoccus sp.

  
 

B. seileri

S11, S14

Bradyrhizobium sp.

  

Rhizobium sp.

  

Burkholderia sp.

  

Candidatus Glomeribacter sp.

  

Polynucleobacter sp.

  

Curvibacter sp.

  

Conchiformibius sp.

  

Snodgrassella sp.

  

Stenoxybacter sp.

  

Tolumonas sp.

  

Idiomarina sp.

  

Photorhabdus sp.

  

Chromohalobacter sp.

  

Balneatrix sp.

  

Oleispira sp.

  

Galeibacterium sp.

  

Pasteurella sp.

  
 

P. muttocida

S11

Anaerocella sp.

  

Myroides sp.

  

Jeotgalicoccus sp.

  

Pseudoflavonifractor sp.

  

Thermobrachium sp.

  

Mobilitalea sp.

  

Marseilibacter sp.

  
 

M. massiliensis

S5, S12

Paeniclostridium sp.

  

Anaerobacterium sp.

  

Holdemania sp.

  

Pedomicrobium sp.

  

Rubellimicrobium sp.

  

Rivibacter sp.

  

Alcaligenes sp.

  

Sulfurimonas sp.

  

Pseudohongiella sp.

  

Zobellella sp.

  

Thiorhodovibrio sp.

  

Providencia sp.

  

neptunomonas sp.

  

Azotobacter sp.

  

Thiopseudomonas sp.

  

Beggiatoa sp.

  

Arenimonas sp.

  

Anaeroplasma sp.

  

Chlamydia sp.

  

Pectinatus sp.

  

Candidatus Gullanella sp.

  

Orbus sp.

  

achromatium sp.

  

Fermentimonas sp.

  

Nitribacter sp.

  

Natranaerovirga sp.

  

Parasporobacterium sp.

  
 

P. paucivorans

S5

Acetanaerobacterium sp.

  

Angelakisella sp.

  
 

A. massiliensis

S5

Ercella sp.

  

Pygmaiobacter sp.

  

Thermodesulfovibrio sp.

  

Caulobacter sp.

  

Candidatus hamiltonella sp.

  

Pyramidobacter sp.

  

Luteipulveratus sp.

  

Aestuarlimicrobium sp.

  
 

A. kwangyangense

S10

Spirosoma sp.

  

Acidibacillus sp.

  

Sinibacillus sp.

  

Solibacillus sp.

  

Carnobacterium sp.

  

Constrictibacter sp.

  

Endozoicomonas sp.

  

Kistimonas sp.

  

Oleiphilus sp.

  

Synergistes sp.

  

Ornithinimicrobium sp.

  

Pseudonocardia sp.

  

Phoenicibacter sp.

  

Cytophaga sp.

  

Alsobacter sp.

  

Rhodobacter sp.

  

Magnetospira sp.

  

Paraglaciecola sp.

  

Candidatus Purcelliella sp.

  
 

P. pentastirinorum

S1

Kosakonia sp.

  

Candidatus Schmidhempelia sp.

  

Parviterribacter sp.

  

Haoranjiania sp.

  

Hathewaya sp.

  

Acidiphilum sp.

  

Sulfurirhabdus sp.

  

Candidatus Regiella sp.

  

Ammoniibacillus sp.

  

Macrococcus sp.

  

Thermoactinomyces sp.

  

Jeotgalibaca sp.

  

Phenylobacterium sp.

  

Cupriavidus sp.

  

Methyloversatalis sp.

  

Desulfuromonas sp.

  

Ferrimonas sp.

  

Vulcaniibacterium sp.

  
  1. Genus marked with an * were found in all the twenty diarrheal samples