The regional landscape of the human colon culturome in health and cystic fibrosis

This pilot study of a small cohort represents the first culturome analysis of the cystic fibrosis colon. Our preliminary findings demonstrate that cystic fibrosis (CF)-associated gut dysbiosis is spatially specific, with mucosal bacterial communities showing pronounced alterations while luminal communities show comparatively subtle phylum-specific shifts. This spatial specificity suggests the mucosal microenvironment as a potential therapeutic target and indicates that interventions focused solely on luminal bacteria may be insufficient. The promising predictive accuracy of culturome-based machine learning models in this small cohort suggests these viable bacterial signatures could serve as biomarkers for CF management pending larger validation studies. Additionally, our initial observations of CFTR modulator effects on gut microbial communities provide insight for future studies optimizing combination therapies.