Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease and its frequent complication with ulcerative colitis (UC) highlights the pathogenic role of epithelial barrier dysfunction. Here, we aimed to identify the specific microbiota that contribute to the pathogenesis of PSC using humanized gnotobiotic mice. We generated gnotobiotic mice by inoculating fecal samples from patients with PSC/UC (PSCUC mice), UC (UC mice), or healthy controls (HC mice). In contrast to other gnotobiotic mice, PSCUC mice demonstrated higher Th17 response in the liver and strong susceptibility to the experimental hepatobiliary inflammation by DDC. We identified three bacterial species, Klebsiella pneumoniae, Proteus mirabilis, and Enterococcus gallinarum from the mesenteric lymph nodes of PSCUC mice by bacterial culture. Importantly, these pathobionts were specifically enriched in the feces of PSC/UC patients. Mono-inoculation with PSC mice-derived K. pneumoniae caused mucosal invasion detected by FISH. Using a culture system with monolayered human intestinal organoids, we demonstrated that PSC/UC-derived K. pneumoniae unlike commercially available K. pneumoniae, induced epithelial-pore formation with apoptosis-related genes upregulation. Finally, antibiotic treatment targeting K. pneumoniae was effective in the reduction of pathogenic Th17 response in the liver in PSCUC mice. Collectively, our results identified specific pathobionts in PSC/UC patients that collude in intestinal barrier disruption and Th17-priming in the liver, and provide insights into the implication of the gut microbiota in the pathogenesis. |