High-resolution metabolomic analysis of stool reveals expanded biomarkers of C. difficile colitis and insights into pathophysiology

Clostridioides difficile infection (CDI) is facilitated by gut microbiome disruption and associated metabolic disturbances. While many prior studies have focused on the microbial composition of CDI stool, fewer have explored the fecal metabolome using untargeted high-resolution metabolomics (HRM). To characterize the metabolic phenotype of CDI, we performed untargeted HRM on stool samples from 55 CDI patients and 72 healthy controls. CDI was associated with marked alterations in stool metabolites, mapping to 14 significantly dysregulated pathways, including tryptophan metabolism, bile acid metabolism, short-chain fatty acid metabolism, and fatty acid oxidation. These findings suggest that CDI is associated with a distinct fecal metabolic milieu that may promote inflammation, impair colonization resistance, and facilitate C. difficile replication. Our results corroborate previous studies and support further investigation of the role of microbial and immune signaling in CDI as well as metabolic biomarkers and therapeutic targets. IMPORTANCE As we learn more about the essential role of gut microbes in human health and disease, there is an effort to identify and characterize stool biomarkers that distinguish patients with microbiome-associated disease from healthy individuals. Clostridioides difficile infection contributes to excess healthcare burden and is tightly linked to disruption of the gut microbiome (usually by use of antimicrobials). We compared the metabolome of healthy stool and C. difficile-infected stool to identify metabolites that correlate with disease and may support the development of improved diagnostic tests for C. difficile infection. In comparing these two groups, we found chemical pathways that strongly correlate with disease and others more associated with healthy stool, including bile acid biosynthesis, tryptophan metabolism, and carnitine activation.