Table 1.
Gut bacteria and the metabolites they contribute
| Metabolite | Pathway | Genera or species | Reference |
|---|---|---|---|
| Butyrate | Classical pathway via butyrate kinase | Coprococcus comes, Coprococcus eutactus | Macfarlane and Macfarlane, 2003, Cummings et al., 1987, den Besten et al., 2013, Smith and Macfarlane, 199716,17,18,19 |
| Alternate pathway using exogenous acetate | Anaerostipes spp., C. catus, E. hallii, Eubacterium rectale, Faecalibacterium prausnitzii, Roseburia spp. | Macfarlane and Macfarlane, 2003, den Besten et al., 2013, Smith and Macfarlane, 1997, Cummings and Macfarlane, 199116,18,19,20 | |
| Propionate | Acrylate pathway | Coprococcus catus, Eubacterium hallii, Megasphaera elsdenii, Veillonella spp. | Macfarlane and Macfarlane, 2003, Cummings et al., 1987, den Besten et al., 2013, Smith and Macfarlane, 199716,17,18,19 |
| Succinate pathway | Bacteroides spp., Dialister spp., Phascolarctobacterium succinatutens, Veillonella spp. | Macfarlane and Macfarlane, 2003, Cummings et al., 1987, den Besten et al., 2013, Smith and Macfarlane, 199716,17,18,19 | |
| Propanediol pathway | Roseburia inulinivorans, Ruminococcus obeum, Salmonella enterica | Macfarlane and Macfarlane, 2003, Cummings et al., 1987, den Besten et al., 2013, Smith and Macfarlane, 199716,17,18,19 | |
| Acetate | Pyruvate decarboxylation to acetyl-CoA | Akkermansia muciniphila, Bacteroides spp., Bifidobacterium spp., Prevotella spp., Ruminococcus spp | Macfarlane and Macfarlane, 2003, Cummings et al., 1987, den Besten et al., 2013, Smith and Macfarlane, 199716,17,18,19 |
| Wood–Ljungdahl pathway | Blautia hydrogenotrophica, Clostridium spp., Streptococcus spp. | Macfarlane and Macfarlane, 2003, Cummings et al., 1987, den Besten et al., 2013, Smith and Macfarlane, 199716,17,18,19 | |
| Branched-chain fatty acids | Amino acid fermentation through various dissimilatory proteolytic reactions | Acidaminococcus spp., Acidaminobacter spp., Campylobacter spp., Clostridia spp., Eubacterium spp., Fusobacterium spp., Peptostreptococcus spp. | Macfarlane and Macfarlane, 2003, Cummings et al., 1987, den Besten et al., 2013, Smith and Macfarlane, 1997, Deehan et al., 202016,17,18,19,21 |
| Imidazole propionate | Non-oxidative deamination of histidine to urocanate followed by reduction of urocanate to ImP by urocanate reductase | Aerococcus urinae, Adlercreutziae equolifaciens, Anaerococcus prevotii, Brevibacillus laterosporus, Eggerthella lenta, Lactobacillus paraplantarum, Shewanella oneidensis, Streptococcus mutans | Koh et al., 201822 |
| Indole | Hydrolytic β-elimination of tryptophan to indole (tryptophanase) | Achromobacter liquefaciens, Bacteroides ovatus, Bacteroides thetaiotamicron, Escherichia coli, Paracolobactrum coliforme, Proteus vulgaris | Devlin et al., 2016, Agus et al., 201823,24 |
| Indole derivatives | Multiple | Bacteroides spp., Clostridium spp. (Clostridium sporogenes, Clostridium cadaveris, Clostridium bartlettii), E. coli, Lactobacillus spp., E. halli, Parabacteroides distasonis, Peptostreptococcus spp. (Peptostreptococcus anaerobius) | Devlin et al., 2016, Agus et al., 2018, Dodd et al., 201723,24,25 |
| Trimethylamine N-oxide | Intestinal bacteria metabolize choline, choline-containing compounds, betaine, and L-carnitine ingested in the diet or recycled in the gut | Desulfovibrio desulfuricans, Acinetobacter, Serratia, Klebsiella pneumoniae, E. coli, Citrobacter, Providencia, Shigella, Achromobacter, Sporosarcina, Actinobacteria, Edwardsiella tarda | Craciun and Balskus, 2012, Thibodeaux and van der Donk, 2012, Falony et al., 2012, Romano et al., 201226,27,28,29 |
| Bile acids | |||
| Primary bile acids | Synthesized in the liver from cholesterol via classical or alternative pathways and bound to taurine or glycine | Host (mouse and human) | Wahlström et al., 2016, Jia et al., 201630,31 |
| Secondary bile acids | Deconjugation of primary and secondary bile acids through bile salt hydrolases | Bacteroides, Bifidobacterium, Clostridium, Eubacterium, Lactobacillus | Wahlström et al., 2016, Jia et al., 201630,31 |
| Conjugation to phenylalanine, tyrosine or leucine | Clostridium bolteae | Quinn et al., 201732 | |
| 7α/β-dehydroxylation; 3α/β-epimerization; 5β/α-epimerization; 6β-epimerization of β-MCA; 7α/β-epimerization of CDCA and β-MCA; oxidation of primary or secondary bile acids at C3, C7, and C12 | Bacteroides, Clostridium, Escherichia, Eubacterium, Lactobacillus; Eubacterium lentum, Clostridium perfringens, Ruminococcus gnavus; Eubacterium; Eubacterium, Fusobacterium, Unidentified Gram-positive rod; Clostridium, Unidentified Gram-positive rod; Bacteroides, Clostridium, Eggerthella, Escherichia, Eubacterium, Peptostreptococcus, Ruminococcus | Wahlström et al., 2016, Jia et al., 2016, Funabashi et al., 2020, Eyssen et al., 1983, Demarne et al., 198230,31,33,34,35 | |