Table 1.

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

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	[36–38]
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	[82–84]
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]