LC/MS Untargeted Metabolomics Peak Areas for Xenometabolomics reveals metabolic functional guilds unique to specific inulin subtypes in human gut microbiota cultures, Piccolo et al, mSystems, 2025

Dietary fibers promote positive health outcomes that are generally attributed to large bowel bacterial fermentation and associated bioactive metabolites. Historically, studies of the latter have focused on short-chain fatty acids such as butyrate. The gastrointestinal microbiota generate thousands of xenometabolites (microbe-derived, “non-host” metabolites). Most remain uncharacterized for composition and potential bioactivity, and little is known about the impact of fiber structure on the xenometabolome. Using LC/MS we characterized culture supernatant metabolite profiles in human stool lineages derived from 3 healthy adult donors and 6 inulins covering a range of degrees of polymerization (DPs): chicory-derived Frutalose L90 (L90; DP ~ 3), Alfa Aesar (AA; DP ~5), Frutafit CLR (CLR; DP ~ 8), Frutafit IQ (IQ; DP ~12), Frutafit TEX (TEX; DP > 23), and the highly branched Frutafit agave inulin (AGA). Of the 1219 LC/MS detected metabolites included in the final data analysis, concentrations of 704 were statistically significant (FDR < 0.1; Kruskal-Wallis test); of these, 17 metabolites had a structural annotation, highlighting the large number of “unknown” xenometabolites associated with inulin substrates. Each fiber type led to distinct metabolite signatures despite lineages displaying highly disparate microbial community structures within and across donors. This illustrates that fiber-specific metabolic functional guilds manifest despite highly diverse human gut bacteria communities. While speculative, the metabolic functional guilds could help explain why health effects of dietary fibers are prevalent across the population despite highly disparate gut microbiota patterns. The results also reinforce that fiber structures have a profound effect on the xenometabolome.