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BACKGROUND: Human 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.RESULTS: By 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.CONCLUSIONS: We 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.