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Table 1 Substrates consumed by major commensal microbial species to produce metabolites in the human gut

From: The impact of gut microbiota metabolites on cellular bioenergetics and cardiometabolic health

Substrate Genus (species) Metabolite References
Acetate Faecalibacterium (F. prausnitzii)
Eubacterium (E. rectale, E. halii)
Roseburia (R. intestinalis, R. hominis, R. inulinivorans)
Anaerostipes (A. hadrus)
Coprococcus (C. catus)
Butyrate [36,37,38]
Succinate Bacteroides (B. uniformis, B. vulgates)
Prevotella (P. copri)
Alistipes (A. putredinis)
Ruminococcus (R. flavefaciens)
Phascolarctobacterium (P. succinatutens)
Dialister (D. invisus)
Akkermansia (A. muciniphila)
Propionate [38]
Acrylate Megasphaera (M. elsdenii)
Coprococcus (C. catus)
Propionate [38]
Fucose
or rhamnose
Roseburia (R. inulinivorans)
Eubacterium (E. hallii)
Blautia (B. obeum)
Propionate [38]
Pyruvate Bacteroides (B. frragilis, B. ovatus)
Bifidobacterium (B. adolescentis, B. longum)
Clostridium (C. perfringens, C. bifermentans)
Ruminococcus (R. bromii, R. gnavus)
Acetate [42, 43]
Sulfate Desulfovibrio (D. piger, D. desulfuricans) H2S [46]
Sulfite Escherichia (E. coli) H2S [49]
Cysteine Escherichia (E. coli)
Enterobacter (E. aerogenes, E. cloacae)
H2S [50]
Thiosulfate Citrobacter (C. freundii)
Proteus (P. vulgaris)
Edwardsiella (E. tarda)
H2S [56]
Nitrite Lactobacillus (L. acidophilus, L. shirota, L. rhamnosus)
Bifidobacterium (B. bifidus, B. breve, B. infantis)
NO [81]
Arginine Bacillus (B. subtilis, B. anthracis)
Deinococcus (D. radiodurans)
NO [82,83,84]
Formate Methaninobrevibacter (M. smithii) Methane [95]
Methanol Methanosphaera (M. stadtmanae) Methane [94]
Choline Anaerococcus (A. hydrogenalis)
Clostridium (C. asparagiforme, C. hathewayi, C. sporogenes)
Desulfitobacterium (D. hafniense)
Escherichia (E. fergusonii)
Proteus (P. penneri)
Providencia (P. rettgeri, P. alcalifaciens, P. rustigianii)
Edwardsiella (E. tarda)
Yokenella (Y. regensburgei)
TMA [98, 99]
Carnitine Citrobacter (C. freundii)
Escherichia (E. coli)
Proteus (P. vulgaris)
TMA [99]