Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease

Children with inflammatory bowel diseases (IBD) are particularly vulnerable to infection with Clostridioides difficile (CDI). IBD and IBD + CDI have overlapping symptoms but respond to distinctive treatments, highlighting the need for diagnostic biomarkers. Here, we studied pediatric patients with IBD and IBD + CDI, comparing longitudinal data on the gut microbiome, metabolome, and other measures. The microbiome is dysbiotic and heterogeneous in both disease states, but the metabolome reveals disease-specific patterns. The IBD group shows increased concentrations of markers of inflammation and tissue damage compared with healthy controls, and metabolic changes associate with susceptibility to CDI. In IBD + CDI, we detect both metabolites associated with inflammation/tissue damage and fermentation products produced by C. difficile. The most discriminating metabolite found is isocaproyltaurine, a covalent conjugate of a distinctive C. difficile fermentation product (isocaproate) and an amino acid associated with tissue damage (taurine), which may be useful as a joint marker of the two disease processes. [Display omitted] •Multi-omics reveals markers of CDI in pediatric IBD patients•Identification of metabolites reveals distinctive features for IBD and CDI•Isocaproyltaurine is made by C. difficile and associates with active IBD•Identifies biomarkers potentially useful for distinguishing disease processes Children with inflammatory bowel diseases (IBD) are prone to infection with C. difficile (CDI). Bushman et al. report the microbiome and metabolome of children with IBD or IBD + CDI, revealing distinctive metabolites associated with the two disease processes that may be useful as biomarkers to guide targeted therapy.