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

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]