Key metabolites
Health-relevant gut metabolites and which reconstructions are predicted to secrete or take them up. Predicted capability (max potential, unlimited medium; APOLLO + AGORA2) — not measured. Click a metabolite for its page, or “rank microbes” to browse producers/consumers.
Short-chain fatty acids & fermentation products
Major end-products of gut fermentation — energy for the host, immune and metabolic signalling, and the currency of microbial cross-feeding.
Primary energy source for colonocytes; anti-inflammatory.
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Gluconeogenesis substrate; appetite & lipid regulation.
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Most abundant SCFA; cross-fed to butyrate producers.
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Fermentation intermediate; cross-fed onward to SCFAs.
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Propionate precursor; raised in some dysbioses.
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Fermentation product; interspecies electron transfer.
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Gases & nitrogen
Products of protein/sulfur metabolism with host-health relevance.
Genotoxic at high levels; linked to colitis & CRC.
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Protein-fermentation product; hepatic/colonic relevance.
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B vitamins
Microbial synthesis contributes to the host's vitamin supply; many taxa are auxotrophs that rely on cross-feeding.
Few microbes synthesise it; heavily cross-fed.
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Microbial folate adds to host supply.
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Redox cofactor & electron shuttle.
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Essential cofactor; many microbes are auxotrophs.
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Carboxylation cofactor; commonly cross-fed.
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Amino-acid metabolism cofactor.
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Neurotransmitters & gut–brain metabolites
Neuroactive compounds (and microbial precursors/catabolites) that underlie microbial influence on the gut–brain axis.
Main inhibitory neurotransmitter (4-aminobutyrate).
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Monoamine neurotransmitter; mostly gut-associated.
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Direct serotonin precursor.
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Trace amine; tyrosine-derived.
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Biogenic amine; immune & neuro signalling.
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Main excitatory neurotransmitter.
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Precursor of serotonin / kynurenine / indoles.
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Microbial Trp catabolite; gut–brain signalling.
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Microbial Trp catabolite; AhR ligand.
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Microbial tyrosine catabolite; neuro-relevant.
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Amino acids
The 20 proteinogenic amino acids — fermentation substrates and products; aromatics and glutamate/glycine double as neurotransmitter precursors or signals.
Glucogenic; alanine cycle.
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NO & polyamine precursor.
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Excitatory; urea/TCA links.
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Sulfur AA; glutathione & H₂S.
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Excitatory NT; also an amino acid.
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Inhibitory NT; one-carbon metabolism.
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Aromatic; catecholamine precursor.
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Essential; mucin glycoprotein.
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Serotonin / indole precursor.
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Dopamine / catecholamine precursor.
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Source: Supplementary Table S3 of Heinken A, Hulshof TO, Nap B, … Thiele I. A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes… Cell Systems 2025;16(2):101196. PMID: 39947184.
