High thrombin activity associated with crohn’s disease induces microbiota pathogenicity contributing to mucosal inflammation

Thrombin is a serine protease produced by the intestinal epithelium that contributes to mucosal homeostasis by limiting microbial encroachment. In Crohn's disease, mucosal thrombin activity is markedly increased, suggesting a role in disease pathophysiology. We hypothesized that excessive luminal thrombin disrupts host–microbiota interactions and promotes a pathogenic microbial phenotype. Thrombin levels were significantly elevated in fecal samples from a subset of Crohn's disease patients compared with healthy controls. Ex vivo experiments using human colonic biopsy-derived microbiota, cultured as polymicrobial biofilms, revealed that thrombin exposure disrupted biofilm integrity, enriched the protein-rich extracellular matrix, and promoted bacterial dispersal. Dispersed bacteria displayed enhanced adhesion to intestinal epithelial cells and triggered inflammatory and antimicrobial responses through Toll-Like Receptor 5 signaling. Although the global taxonomic composition showed limited changes, metatranscriptomic analyses demonstrated distinct microbial activity profiles in the presence of thrombin. In vivo, intracolonic thrombin altered mucosal biofilm organization in mice, and the transfer of thrombin-exposed mucosal microbiota to germ-free recipients induced mucosal inflammation and bacterial translocation. Finally, in a rat model of colitis, pharmacological inhibition of thrombin activity restored mucosal biofilm architecture and reduced tissue damage. These findings identify thrombin as a host-associated modulator of microbial functional dysbiosis in patients with Crohn's disease. By driving a shift toward a pathogenic microbial phenotype, excessive thrombin links epithelial activity with altered host–microbiota interactions and mucosal inflammation. Thrombin measurement in fecal samples may represent a non-invasive marker of microbiota pathogenicity, and therapeutic targeting of thrombin offers a promising complementary strategy to immune-directed treatments in Crohn's disease.