Supplementation with endogenous healthy gut metabolites reverses the disruptions of in vitro and ex vivo epithelial functions induced by fecal content from IBD patients.

Despite epithelial involvement in inflammatory bowel disease (IBD) pathogenesis and the gaps in treatment goals with existing immune-directed therapy, epithelial-directed interventions are unavailable. Using patient-based models, we aimed to identify bioactive endogenous metabolites that can improve IBD epithelial dysfunction, are generally regarded as safe, and can enhance epithelial homeostasis. We pooled fecal material from subjects with and without IBD to capture patient heterogeneity and analyzed the fecal contents for microbiome composition and metabolomics. Epithelial cells (Caco-2 cells and patient-derived colonoids) were cultured, and fecal material was applied apically to replicate the gut's physiological orientation. Measurable epithelial outputs included epithelial proinflammatory signals, integrity, and cellular ATP levels. We show that fecal content pools from several independent IBD patients disturb epithelial functions significantly more than does the fecal content from controls. Improved epithelial readouts in the functional patient-based models were linked with several gut metabolite levels, and these findings were further validated in an independent published human biospecimen multi-omics in vivo cohort. This guided the supplementation of five prioritized metabolites (azelate, pyridoxal, fructose-6-phosphate, galactose 1-phosphate, and ribose 5-phosphate) into the IBD fecal content, which reversed the related IBD epithelial dysfunction. We streamline a proof-of-concept pipeline for the prioritization of epithelial-targeted metabolite interventions that can direct safe future novel adjunct interventions.