Supplementary Table 1: List of the Prokaryotes Growing Aerobically in R-Medium

Supplementary Table 1: List of the prokaryotes growing aerobically in R-medium.

Supplementary Table 1A: Strict anaerobic bacterial species

Phylum / Genus / Species / No of Strains / Growth time
Actinobacteria / Bifidobacterium / Bifidobacterium adolescentis / 1 / 72H
Bifidobacterium brevis / 1 / 72H
Bifidobacterium catenulatum / 1 / 72H
Bifidobacterium longum / 1 / 72H
Bifidobacterium pseudocatenulatum / 1 / 72H
Collinsella / Collinsella aerofaciens / 1 / 96H
Collinsella massilioamazoniensis / 2 / 72H
Collinsella tanakaei / 2 / 96H
Eggerthella / Eggerthella lenta / 2 / 48H
Gordonibacter / Gordonibacter pamelaeae / 1 / 72H
Bacteroidetes / Alistipes / Alistipes finegoldii / 2 / 96H
Alistipes indistinctus / 2 / 96H
Alistipes putredinis / 1 / 96H
Alistipes shahii / 2 / 96H
Bacteroides / Bacteroides caccae / 6 / 72H
Bacteroides fragilis / 2 / 48H
Bacteroides intestnalis / 3 / 48H
Bacteroides nordii / 1 / 48H
Bacteroides ovatus / 2 / 48H
Bacteroides stercoris / 1 / 48H
Bacteroides thetaiotaomicron / 2 / 48H
Bacteroides timonensis / 1 / 72H
Bacteroides uniformis / 2 / 48H
Bacteroides vulgatus / 1 / 48H
Barnesiella / Barnesiella intestinihominis / 2 / 48H
Odoribacter / Odoribacter splanchnicus / 1 / 48H
Parabacteroides / Parabacteroides distasonis / 1 / 48H
Parabacteroides johnsonii / 1 / 48H
Parabacteroides merdae / 1 / 48H
Porphyromonas / Porphyromonas asaccharolityca / 1 / 72H
Prevotella / Prevotella buccalis / 1 / 72H
Firmicutes / Acidaminococcus / Acidaminococcus intestini / 2 / 48H
Amazonia / Amazonia massiliensis / 1 / 48H
Anaerococcus / Anaerococcus vaginalis / 5 / 72H
Anaerosalibacter / Anaerosalibacter bizertensis / 2 / 72H
Anaerosalibacter massiliensis / 1 / 72H
Blautia / Blautia coccoides / 1 / 96H
Clostridium / Clostridium amazonitimonense / 1 / 72H
Clostridium amylolyticum / 1 / 72H
Clostridium anorexicamassiliensis / 2 / 72H
Clostridium anorexicus / 1 / 72H
Clostridium baratii / 1 / 72H
Clostridium bartlettii / 1 / 72H
Clostridium bifermentans / 1 / 72H
Clostridium bolteae / 1 / 72H
Clostridium butyricum / 4 / 72H
Clostridium clostridioforme / 1 / 72H
Clostridium cochlearium / 1 / 72H
Clostridium dakarense / 1 / 72H
Clostridium difficile / 6 / 96H
Clostridium glycolicum / 2 / 72H
Clostridium hathewayi / 3 / 48H
Clostridium jeddahense / 2 / 72H
Clostridium lituseburense / 1 / 72H
Clostridium paraputrificum / 2 / 72H
Clostridium perfringens / 2 / 72H
Clostridium ramosum / 1 / 72H
Clostridium rubiinfantis / 1 / 72H
Clostridium sartagoforme / 1 / 72H
Clostridium senegalense / 2 / 72H
Clostridium sordellii / 1 / 48H
Clostridium sporogenes / 3 / 72H
Clostridium subterminale / 3 / 72H
Clostridium symbiosum / 1 / 72H
Clostridium tertium / 2 / 48H
Dielma / Dielma fastidiosa / 1 / 48H
Finegoldia / Finegoldia magna / 1 / 48H
Flavonifractor / Flavonifractor plautii / 2 / 48H
Guyana / Guyana massiliensis / 1 / 72H
Holdemania / Holdemania massiliensis / 1 / 72H
Parvimonas / Parvimonas micra / 1 / 72H
Peptoniphilus / Peptoniphilus asaccharolyticus / 3 / 72H
Peptoniphilus harei / 3 / 72H
Peptoniphilus senegalensis / 2 / 72H
Peptostreptococcus / Peptostreptococcus asaccharolyticus / 1 / 72H
Ruminococcus / Ruminococcus gnavus / 1 / 48H
Tissierella / Tissierella praeacuta / 1 / 72H
Turicibacter / Turicibacter sanguinis / 1 / 72H
Veillonella / Veillonella dispar / 2 / 48H
Veillonella parvula / 1 / 48H
Fusobacteria / Fusobacterium / Fusobacterium necrophorum / 2 / 48H
Fusobacterium nucleatum / 1 / 48H
82 Species / 135 Strains

Supplementary Table 1B: Facultative anaerobic bacterial species (excepted fastidious bacteria: see Table 1E)

Phylum / Genus / Species / No of Strains / Growth time
Actinobacteria / Actinomyces / Actinomyces neuii / 2 / 48H
Actinomyces oris / 4 / 48H
Actinomyces radingae / 1 / 48H
Actinomyces urogenitalis / 1 / 48H
Corynebacterium / Corynebacterium accolens / 2 / 48H
Corynebacterium afermentans / 5 / 48H
Corynebacterium amycolatum / 3 / 48H
Corynebacterium aurimucosum / 1 / 48H
Corynebacterium efficiens / 1 / 48H
Corynebacterium jeikeium / 2 / 48H
Corynebacterium minutissimum / 1 / 48H
Corynebacterium propinquum / 1 / 48H
Corynebacterium pseudodiphtheriticum / 4 / 48H
Corynebacterium simulans / 2 / 48H
Corynebacterium striatum / 2 / 48H
Corynebacterium suicordis / 1 / 48H
Corynebacterium urealyticum / 2 / 48H
Corynebacterium ihumii / 1 / 48H
Corynebacterium tuberculostearicum / 3 / 48H
Corynebacterium ureicelerivorans / 1 / 48H
Dermabacter / Dermabacter hominis / 2 / 48H
Gardnerella / Gardnerella vaginalis / 2 / 24H
Propionibacterium / Propionibacteriumacnes / 4 / 24H
Propionibacterium avidum / 2 / 24H
Rothia / Rothia aeria / 1 / 48H
Rothia dentocariosa / 2 / 24H
Firmicutes / Aerococcus / Aerococcus urinae / 2 / 48H
Aerococcus viridans / 2 / 48H
Aneurinibacillus / Aneurinibacillus migulanus / 1 / 24H
Bacillus / Bacillus amyloliquefaciens / 2 / 36H
Bacillus aquimaris / 1 / 48H
Bacillus arsenicus / 1 / 24H
Bacillus badius / 1 / 24H
Bacillus bataviensis / 1 / 24H
Bacillus cereus / 1 / 24H
Bacillus circulans / 1 / 24H
Bacillus clausii / 1 / 24H
Bacillus coagulans / 1 / 24H
Bacillus firmus / 3 / 24H
Bacillus flexus / 4 / 24H
Bacillus koreensis / 1 / 24H
Bacillus lentus / 1 / 24H
Bacillus licheniformis / 4 / 24H
Bacillus massilioamazoniensis / 1 / 24H
Bacillus megaterium / 1 / 24H
Bacillus mojavensis / 1 / 24H
Bacillus oleronius / 1 / 24H
Bacillus pumilus / 3 / 24H
Bacillus rubiinfantis / 1 / 24H
Bacillus siralis / 4 / 24H
Bacillus subtilis / 6 / 24H
Bacillus thermoamylovorans / 3 / 24H
Bacillus vallismortis / 1 / 24H
Enterococcous / Enterococcus avium / 9 / 24H
Enterococcus casseliflavus / 3 / 24H
Enterococcus cecorum / 1 / 24H
Enterococcus dispar / 2 / 24H
Enterococcus durans / 9 / 24H
Enterococcus faecalis / 13 / 24H
Enterococcus faecium / 10 / 24H
Enterococcus gallinarum / 9 / 24H
Enterococcus hirae / 7 / 24H
Enterococcus malodoratus / 2 / 24H
Enterococcus phoeniculicola / 1 / 24H
Enterococcus pseudoavium / 1 / 24H
Enterococcus raffinosus / 1 / 24H
Eubacterium / Eubacterium limosum / 2 / 24H
Eubacterium tenue / 2 / 24H
Gemella / Gemella morbillorum / 2 / 24H
Granulicatella / Granulicatella elegans / 1 / 72H
Lactobacillus / Lactobacillus agilis / 3 / 24H
Lactobacillus fermentum / 3 / 24H
Lactobacillus gasseri / 1 / 24H
Lactobacillus johnsonii / 1 / 24H
Lactobacillus kalixensis / 1 / 24H
Lactobacillus mucosae / 2 / 24H
Lactobacillus paracasei / 2 / 24H
Lactobacillus plantarum / 2 / 24H
Lactobacillus reuteri / 3 / 24H
Lactobacillus sakei / 4 / 24H
Lactococcus / Lactococcus garvieae / 1 / 24H
Lactococcus lactis / 1 / 24H
Lysinibacillus / Lysinibacillus boronitolerans / 2 / 24H
Lysinibacillus fusiformis / 1 / 24H
Lysinibacillus meyeri / 1 / 24H
Lysinibacillus sphaericus / 2 / 24H
Paenibacillus / Paenibacillus lactis / 2 / 48H
Pediococcus / Pediococcus acidilactici / 1 / 48H
Pediococcus pentosaceus / 3 / 48H
Staphylococcus / Staphylococcus aureus / 5 / 24H
Staphylococcus capitis / 6 / 24H
Staphylococcus caprae / 4 / 24H
Staphylococcus cohnii / 5 / 24H
Staphylococcus epidermidis / 2 / 24H
Staphylococcus faecalis / 2 / 24H
Staphylococcus haemolyticus / 3 / 24H
Staphylococcus hominis / 2 / 24H
Staphylococcus intermedius / 3 / 24H
Staphylococcus lugdunensis / 3 / 24H
Staphylococcus pasteuri / 3 / 24H
Staphylococcus pettenkoferi / 2 / 24H
Staphylococcus saprophyticus / 2 / 24H
Staphylococcus schleiferi / 2 / 24H
Staphylococcus simulans / 5 / 24H
Staphylococcus warneri / 4 / 24H
Streptococcus / Streptococcus agalactiae / 3 / 24H
Streptococcus anginosus / 4 / 24H
Streptococcus constellatus / 3 / 24H
Streptococcus cristatus / 3 / 24H
Streptococcus dysgalactiae / 5 / 24H
Streptococcus equinus / 4 / 24H
Streptococcus gallolyticus / 2 / 24H
Streptococcus gordonii / 2 / 24H
Streptococcus intermedius / 3 / 24H
Streptococcus lutetiensis / 7 / 24H
Streptococcus mitis / 5 / 24H
Streptococcus oralis / 5 / 24H
Streptococcus parasanguinis / 4 / 24H
Streptococcus pneumoniae / 3 / 24H
Streptococcus pyogenes / 1 / 24H
Streptococcus salivarius / 2 / 24H
Streptococcus sanguinis / 2 / 48H
Weissella / Weissella cibaria / 2 / 48H
Proteobacteria / Aeromonas / Aeromonas hydrophila / 1 / 48H
Cedecea / Cedecea lapagei / 2 / 24H
Cedecea neteri / 3 / 24H
Citrobacter / Citrobacter braakii / 4 / 24H
Citrobacter freundii / 3 / 24H
Citrobacter koseri / 3 / 24H
Citrobacter sedlakii / 1 / 24H
Enterobacter / Enterobacter aerogenes / 3 / 24H
Enterobacter asburiae / 3 / 24H
Enterobacter cloacae / 5 / 24H
Enterobacter kobei / 2 / 24H
Escherichia / Escherichia coli / 10 / 24H
Hafnia / Hafnia alvei / 3 / 48H
Kingella / Kingella kingae / 1 / 24H
Klebsiella / Klebsiella oxytoca / 2 / 24H
Klebsiella pneumoniae / 3 / 24H
Morganella / Morganella morganii / 2 / 48H
Pasteurella / Pasteurella multocida / 1 / 48H
Proteus / Proteus mirabilis / 2 / 24H
Proteus vulgaris / 3 / 24H
Providencia / Providencia heimbachae / 1 / 24H
Providencia rettgeri / 2 / 24H
Providencia stuartii / 2 / 24H
Serratia / Serratia liquefaciens / 2 / 24H
Serratia marcescens / 3 / 24H
Serratia ureilytica / 1 / 24H
Raoultella / Raoultella ornithinolytica / 1 / 48H
150 Species / 396 Strains

Supplementary Table 1C: Strict aerobic bacterial species (excepted fastidious bacteria: see Table 1E)

Phylum / Genus / Species / No of Strains / Growth time
Actinobacteria / Brevibacterium / Brevibacterium casei / 4 / 24H
Brevibacterium luteolum / 3 / 24H
Brevibacterium ravenspurgense / 1 / 24H
Dietzia / Dietzia cinnamea / 1 / 24H
Kocuria / Kocuria rhizophila / 4 / 24H
Micrococcus / Micrococcus luteus / 7 / 24H
Firmicutes / Gracilibacillus / Gracilibacillus dipsosauri / 2 / 24H
Halobacillus / Halobacillus trueperi / 1 / 24H
Proteobacteria / Achromobacter / Achromobacter xylosoxidans / 2 / 24H
Acinetobacter / Acinetobacter baumannii / 3 / 24H
Acinetobacter lwoffii / 3 / 24H
Acinetobacter pittii / 4 / 24H
Acinetobacter radioresistens / 1 / 24H
Acinetobacter septicus / 2 / 24H
Burkholderia / Burkholderia cepacia / 3 / 24H
Moraxella / Moraxella catarrhalis / 1 / 24H
Neisseria / Neisseria elongata / 3 / 24H
Neisseria flavescens / 3 / 24H
Neisseria gonorrhoeae / 2 / 24H
Neisseria maccacae / 3 / 24H
Neisseria meningitidis / 2 / 24H
Neisseria mucosa / 3 / 24H
Pseudomonas / Pseudomonas aeruginosa / 6 / 24H
Pseudomonas oryzihabitans / 1 / 24H
Pseudomonas putida / 3 / 24H
Pseudomonas saudiphocaensis / 1 / 48H
Roseomonas / Roseomonas mucosa / 1 / 24H
Sphingomonas / Sphingomonas paucimobilis / 2 / 24H
Stenotrophomonas / Stenotrophomonas maltophila / 2 / 24H
29 Species / 74 Strains

Supplementary Table 1D: Microaerophilic bacterial species (excepted fastidious bacteria: see Table 1E)

Phylum / Genus / Species / No of Strains / Growth time
Proteobacteria / Campylobacter / Campylobacter coli / 1 / 48H
Campylobacter concisus / 1 / 48H
Campylobacter fetus / 1 / 48H
Campylobacter jejuni / 1 / 48H
Campylobacter ureolyticum
Firmicutes / Vagococcus / Vagococcus fluvialis / 1 / 48H
6 Species / 6 Strains

Supplementary Table 1E: fastidiousbacterial species

Phylum / Genus / Species / Type of medium / No of Strains / Growth time
AEROBIC
Proteobacteria / Bartonella / Bartonella henselae / R-medium 1bis / 1 / 120H
Eikenella / Eikenella corrodens / R-medium 2 / 1 / 48H
Francisella / Francisella tularensis / R-medium 1 / 1 / 48H
Haemophilus / Haemophilus influenzae / R-medium 2 / 2 / 48H
Haemophilus parainfluenzae / R-medium 2 / 3 / 48H
Legionella / Legionella pneumophila / R-medium 2bis / 1 / 120H
MICROAEROPHILIC
Actinobacteria / Mycobacterium / Mycobacterium bovis / 1 / No growth
Mycobacterium smegmatis / R-medium 1bis / 1 / 96H
Mycobacterium tuberculosis / 1 / No growth

Supplementary Table 1F: Fungi

Phylum / Genus / Species / No of Strains / Growth time
Fungi / Candida / Candida albicans / 1 / 24H
Candida dubliniensis / 1 / 24H
Candida glabrata / 1 / 24H
Candida lusitaniae / 1 / 24H
Candida orthopsilusis / 1 / 24H
Candida parapsilosis / 1 / 24H
Candida tropicalis / 1 / 24H
Kluyveromyces / Kluyveromyces marxianus / 1 / 24H
Pichia / Pichia kudriavzevii / 1 / 24H
Saccharomyces / Saccharomyces cerevisae / 1 / 24H
10 Species / 10 Strains