ArticleMicrobiome2025
Distinguishing diet- and microbe-derived metabolites in the human gut.
Article in Microbiome, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Host-derived Limosilactobacillus reuteri R30 and Cytobacillus solani Y5 improve growth performance and intestinal health of Danzhou chickens by regulating the jejunal microbiota.Poultry science · 2026Article
- Plant-Derived Foods and Medicines as Modulators of the Gut Microbiome: Molecular Interactions and Implications for Disease and Therapy.Molecules (Basel, Switzerland) · 2026Review
- FMT from IBS-D Rats Impairs Intestinal Barrier Function and is Associated with Increased Intestinal Benzoic Acid andJournal of microbiology and biotechnology · 2026Article
- Ketogenic diet-induced changes in hepatic drug metabolism with potential implications for ozanimod pharmacokinetics in mice.PloS one · 2026Article
- Effect ofAnimals : an open access journal from MDPI · 2025Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHuman gut microbes metabolize food and host secretions, consuming and producing small molecules that are important to health and homeostasis. Here, we present an atlas of diet- and microbiome-derived metabolites in the human gut, constructed from a controlled feeding experiment of adults on omnivore and enteral nutrition diets.
resultsBy comparing metabolite concentration before and after microbiome depletion with antibiotics and polyethylene glycol, we identified 2856 microbial products decreasing and 1057 microbial substrates increasing in concentration after depletion. We also identified 2496 diet-derived metabolites by comparing diet groups when the microbiome was depleted. Seven days after antibiotics, 98% of gut metabolites recovered to pre-antibiotic levels in the omnivore group. In plasma samples, only 93 microbiome-derived metabolites varied with gut microbiome depletion, indicating a limited impact on circulating metabolites. To demonstrate our metabolite atlas, we annotated metabolites associated with inflammatory bowel disease and identified the microbiome-derived metabolites altered in gut dysbiosis.
conclusionsWe identified metabolites associated with the metabolism of the human gut microbiome, mapping its overall metabolic potential. Furthermore, we measured the rate at which metabolites were recovered following gut microbiome disruption.
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