From microbes to molecules: mechanistic insights into metabolite-mediated gut inflammation

Microbial metabolites are now recognized as central mediators of host–microbe communication that shape intestinal immune homeostasis and influence the development of inflammatory gastrointestinal diseases. The objective of this review is to synthesize current mechanistic evidence on how microbiota-derived metabolites regulate epithelial and immune functions in the gut, with a focus on metabolite-driven inflammatory pathways. In the healthy intestine, short-chain fatty acids (SCFAs), indole derivatives, secondary bile acids, and polyamines support epithelial integrity, regulate mucosal immunity, and maintain metabolic balance. SCFAs, particularly butyrate, attenuate inflammation by serving as an energy source for colonocytes, inhibiting histone deacetylases, activating G protein-coupled receptors (GPCRs; GPR41, GPR43, GPR109A), and reinforcing epithelial barrier function. In parallel, microbial tryptophan metabolites such as indole-3-propionic acid and indole-3-aldehyde activate aryl hydrocarbon receptor signaling, promoting IL-22 production, antimicrobial peptide expression, and Th17–Treg balance. In inflammatory bowel disease, dysbiosis disrupts these protective pathways, leading to depletion of SCFA- and indole-producing taxa and accumulation of pro-inflammatory metabolites such as succinate. These metabolic shifts impair epithelial-immune crosstalk, amplify NF-κB-dependent inflammation, and compromise mucosal repair. Therapeutic strategies targeting microbial metabolites, including precision prebiotics, next-generation probiotics, engineered microbial consortia, and postbiotics, show translational promise. However, their clinical application remains constrained by interindividual variability, incomplete causal resolution, and challenges in targeted delivery. Integrative multi-omics approaches and mechanistically informed models are therefore essential to advance metabolite-based diagnostics and therapies for gut inflammation.