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Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis


Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease and its frequent complication with ulcerative colitis highlights the pathogenic role of epithelial barrier dysfunction. Intestinal barrier dysfunction has been implicated in the pathogenesis of PSC, yet its underlying mechanism remains unknown. Here, we identify Klebsiella pneumonia in the microbiota of patients with PSC and demonstrate that K.pneumoniae disrupts the epithelial barrier to initiate bacterial translocation and liver inflammatory responses. Gnotobiotic mice inoculated with PSC-derived microbiota exhibited T helper 17 (TH17) cell responses in the liver and increased susceptibility to hepatobiliary injuries. Bacterial culture of mesenteric lymph nodes in these mice isolated K.pneumoniae, Proteus mirabilis and Enterococcus gallinarum, which were prevalently detected in patients with PSC. A bacterial-organoid co-culture system visualized the epithelial-damaging effect of PSC-derived K.pneumoniae that was associated with bacterial translocation and susceptibility to TH17-mediated hepatobiliary injuries. We also show that antibiotic treatment ameliorated the TH17 immune response induced by PSC-derived microbiota. These results highlight the role of pathobionts in intestinal barrier dysfunction and liver inflammation, providing insights into therapeutic strategies for PSC.

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Fig. 1: Magnitude of TH17 priming in the liver and colon of gnotobiotic mice transplanted with human faecal samples.
Fig. 2: Increased susceptibility to DDC-induced hepatobiliary injury in PSCUC mice.
Fig. 3: Gnotobiotic mice with PSC/UC microbiota identified specific bacterial species associated with PSC/UC from the MLN.
Fig. 4: Inhibition of ROR-γt protects mice from DDC-induced hepatobiliary injury.
Fig. 5: K.pneumoniae derived from the MLNs of PSCUC mice induces epithelial pore formation of colonic epithelial cells.
Fig. 6: Bacterial translocation and TH17 priming in the liver are dependent on K.pneumoniae strains.

Data availability

The data supporting the findings of this study are available from the corresponding authors upon request. 16S rRNA sequencing and whole-genome sequencing data have been deposited in the DNA Data Bank of Japan (DDBJ) database with the accession numbers DRA007475 and DRA007476 for 16S rRNA sequencing and PRJDB7545 for whole-genome sequencing. RNA sequencing data have been deposited in the European Genome-phenome Archive (EGA) database with the accession number EGAS00001003332.


  1. 1.

    Lazaridis, K. N. & LaRusso, N. F. Primary sclerosing cholangitis. N. Engl. J. Med. 375, 1161–1170 (2016).

    Article  Google Scholar 

  2. 2.

    Horsley-Silva, J. L., Carey, E. J. & Lindor, K. D. Advances in primary sclerosing cholangitis. Lancet Gastroenterol. Hepatol. 1, 68–77 (2016).

    Article  Google Scholar 

  3. 3.

    Hirschfield, G. M., Karlsen, T. H., Lindor, K. D. & Adams, D. H. Primary sclerosing cholangitis. Lancet 382, 1587–1599 (2013).

    Article  Google Scholar 

  4. 4.

    Dyson, J. K., Beuers, U., Jones, D. E. J., Lohse, A. W. & Hudson, M. Primary sclerosing cholangitis. Lancet 391, 2547–2559 (2018).

    Article  Google Scholar 

  5. 5.

    O’Toole, A. et al. Primary sclerosing cholangitis and disease distribution in inflammatory bowel disease. Clin. Gastroenterol. Hepatol. 10, 439–441 (2012).

    Article  Google Scholar 

  6. 6.

    Sasatomi, K., Noguchi, K., Sakisaka, S., Sata, M. & Tanikawa, K. Abnormal accumulation of endotoxin in biliary epithelial cells in primary biliary cirrhosis and primary sclerosing cholangitis. J. Hepatol. 29, 409–416 (1998).

    CAS  Article  Google Scholar 

  7. 7.

    Katt, J. et al. Increased T helper type 17 response to pathogen stimulation in patients with primary sclerosing cholangitis. Hepatology 58, 1084–1093 (2013).

    CAS  Article  Google Scholar 

  8. 8.

    Loftus, E. V. Jr, Sandborn, W. J., Lindor, K. D. & Larusso, N. F. Interactions between chronic liver disease and inflammatory bowel disease. Inflamm. Bowel Dis. 3, 288–302 (1997).

    Article  Google Scholar 

  9. 9.

    Loftus, E. V. et al. PSC-IBD: a unique form of inflammatory bowel disease associated with primary sclerosing cholangitis. Gut 54, 91–96 (2005).

    Article  Google Scholar 

  10. 10.

    Claessen, M. M. et al. More right-sided IBD-associated colorectal cancer in patients with primary sclerosing cholangitis. Inflamm. Bowel Dis. 15, 1331–1336 (2009).

    CAS  Article  Google Scholar 

  11. 11.

    Karlsen, T. H. & Boberg, K. M. Update on primary sclerosing cholangitis. J. Hepatol. 59, 571–582 (2013).

    Article  Google Scholar 

  12. 12.

    Sabino, J. et al. Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD. Gut 65, 1681–1689 (2016).

    CAS  Article  Google Scholar 

  13. 13.

    Kummen, M. et al. The gut microbial profile in patients with primary sclerosing cholangitis is distinct from patients with ulcerative colitis without biliary disease and healthy controls. Gut 66, 611–619 (2017).

    Article  Google Scholar 

  14. 14.

    Iwasawa, K. et al. Characterisation of the faecal microbiota in Japanese patients with paediatric-onset primary sclerosing cholangitis. Gut 66, 1344–1346 (2017).

    Article  Google Scholar 

  15. 15.

    Atarashi, K. et al. Th17 cell induction by adhesion of microbes to intestinal epithelial cells. Cell 163, 367–380 (2015).

    CAS  Article  Google Scholar 

  16. 16.

    Pollheimer, M. J., Trauner, M. & Fickert, P. Will we ever model PSC?—“It’s hard to be a PSC model!”. Clin. Res. Hepatol. Gastroenterol. 35, 792–804 (2011).

    Article  Google Scholar 

  17. 17.

    Tephly, T. R., Gibbs, A. H. & De Matteis, F. Studies on the mechanism of experimental porphyria produced by 3,5-diethoxycarbonyl-1,4-dihydrocollidine. Role of a porphyrin-like inhibitor of protohaem ferro-lyase. Biochem. J. 180, 241–244 (1979).

    CAS  Article  Google Scholar 

  18. 18.

    Fickert, P. et al. A new xenobiotic-induced mouse model of sclerosing cholangitis and biliary fibrosis. Am. J. Pathol. 171, 525–536 (2007).

    CAS  Article  Google Scholar 

  19. 19.

    Atarashi, K. et al. Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation. Science 358, 359–365 (2017).

    CAS  Article  Google Scholar 

  20. 20.

    Bajer, L. et al. Distinct gut microbiota profiles in patients with primary sclerosing cholangitis and ulcerative colitis. World J. Gastroenterol. 23, 4548–4558 (2017).

    CAS  Article  Google Scholar 

  21. 21.

    Withers, D. R. et al. Transient inhibition of ROR-γt therapeutically limits intestinal inflammation by reducing TH17 cells and preserving group 3 innate lymphoid cells. Nat. Med. 22, 319–323 (2016).

    CAS  Article  Google Scholar 

  22. 22.

    In, J. et al. Enterohemorrhagic Escherichia coli reduce mucus and intermicrovillar bridges in human stemcell-derived colonoids. Cell. Mol. Gastroenterol. Hepatol. 2, 48–62 (2016).

    Article  Google Scholar 

  23. 23.

    Sato, T. et al. Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett’s epithelium. Gastroenterology 141, 1762–1772 (2011).

    CAS  Article  Google Scholar 

  24. 24.

    Shneider, M. M. et al. PAAR-repeat proteins sharpen and diversify the type VI secretion system spike. Nature 500, 350–353 (2013).

    CAS  Article  Google Scholar 

  25. 25.

    Russell, A. B., Peterson, S. B. & Mougous, J. D. Type VI secretion system effectors: poisons with a purpose. Nat. Rev. Microbiol. 12, 137–148 (2014).

    CAS  Article  Google Scholar 

  26. 26.

    Siu, L. K., Yeh, K. M., Lin, J. C., Fung, C. P. & Chang, F. Y. Klebsiella pneumoniae liver abscess: a new invasive syndrome. Lancet Infect. Dis. 12, 881–887 (2012).

    Article  Google Scholar 

  27. 27.

    Murray, B. E. The life and times of the Enterococcus. Clin. Microbiol. Rev. 3, 46–65 (1990).

    CAS  Article  Google Scholar 

  28. 28.

    Wiest, R., Lawson, M. & Geuking, M. Pathological bacterial translocation in liver cirrhosis. J. Hepatol. 60, 197–209 (2014).

    Article  Google Scholar 

  29. 29.

    Llorente, C. & Schnabl, B. The gut microbiota and liver disease. Cell. Mol. Gastroenterol. Hepatol. 1, 275–284 (2015).

    Article  Google Scholar 

  30. 30.

    Miele, L. et al. Increased intestinal permeability and tight junction alterations in nonalcoholic fatty liver disease. Hepatology 49, 1877–1887 (2009).

    CAS  Article  Google Scholar 

  31. 31.

    Steffen, E. K., Berg, R. D. & Deitch, E. A. Comparison of translocation rates of various indigenous bacteria from the gastrointestinal tract to the mesenteric lymph node. J. Infect. Dis. 157, 1032–1038 (1988).

    CAS  Article  Google Scholar 

  32. 32.

    Tang, R. et al. Gut microbial profile is altered in primary biliary cholangitis and partially restored after UDCA therapy. Gut 67, 534–541 (2018).

    CAS  Article  Google Scholar 

  33. 33.

    Jiang, F., Waterfield, N. R., Yang, J., Yang, G. & Jin, Q. A Pseudomonas aeruginosa type VI secretion phospholipase D effector targets both prokaryotic and eukaryotic cells. Cell Host Microbe 15, 600–610 (2014).

    CAS  Article  Google Scholar 

  34. 34.

    Alcoforado Diniz, J., Liu, Y. C. & Coulthurst, S. J. Molecular weaponry: diverse effectors delivered by the type VI secretion system. Cell. Microbiol. 17, 1742–1751 (2015).

    CAS  Article  Google Scholar 

  35. 35.

    Spadoni, I. et al. A gut–vascular barrier controls the systemic dissemination of bacteria. Science 350, 830–834 (2015).

    CAS  Article  Google Scholar 

  36. 36.

    Manfredo Vieira, S. et al. Translocation of a gut pathobiont drives autoimmunity in mice and humans. Science 359, 1156–1161 (2018).

    CAS  Article  Google Scholar 

  37. 37.

    Tabibian, J. H. et al. Randomised clinical trial: vancomycin or metronidazole in patients with primary sclerosing cholangitis—a pilot study. Aliment. Pharmacol. Ther. 37, 604–612 (2013).

    CAS  Article  Google Scholar 

  38. 38.

    Hueber, W. et al. Secukinumab, a human anti-IL-17A monoclonal antibody, for moderate to severe Crohn’s disease: unexpected results of a randomised, double-blind placebo-controlled trial. Gut 61, 1693–1700 (2012).

    CAS  Article  Google Scholar 

  39. 39.

    Colombel, J. F., Sendid, B., Jouault, T. & Poulain, D. Secukinumab failure in Crohn’s disease: the yeast connection? Gut 62, 800–801 (2013).

    CAS  Article  Google Scholar 

  40. 40.

    McGeachy, M. J. GM-CSF: the secret weapon in the TH17 arsenal. Nat. Immunol. 12, 521–522 (2011).

    CAS  Article  Google Scholar 

  41. 41.

    Korn, T., Bettelli, E., Oukka, M. & Kuchroo, V. K. IL-17 and Th17 cells. Annu. Rev. Immunol. 27, 485–517 (2009).

    CAS  Article  Google Scholar 

  42. 42.

    Ivanov, I. I. et al. The orphan nuclear receptor RORγt directs the differentiation program of proinflammatory IL-17+ T helper cells. Cell 126, 1121–1133 (2006).

    CAS  Article  Google Scholar 

  43. 43.

    Gaffen, S. L., Jain, R., Garg, A. V. & Cua, D. J. The IL-23–IL-17 immune axis: from mechanisms to therapeutic testing. Nat. Rev. Immunol. 14, 585–600 (2014).

    CAS  Article  Google Scholar 

  44. 44.

    Xiao, S. et al. Small-molecule RORγt antagonists inhibit T helper 17 cell transcriptional network by divergent mechanisms. Immunity 40, 477–489 (2014).

    CAS  Article  Google Scholar 

  45. 45.

    Fujii, M. et al. A colorectal tumor organoid library demonstrates progressive loss of niche factor requirements during tumorigenesis. Cell Stem Cell 18, 827–838 (2016).

    CAS  Article  Google Scholar 

  46. 46.

    Mihara, E. et al. Active and water-soluble form of lipidated Wnt protein is maintained by a serum glycoprotein afamin/alpha-albumin. eLife 5, e11621 (2016).

    Article  Google Scholar 

  47. 47.

    Nishijima, S. et al. The gut microbiome of healthy Japanese and its microbial and functional uniqueness. DNA Res. 23, 125–133 (2016).

    CAS  Article  Google Scholar 

  48. 48.

    Jackson, C. R., Fedorka-Cray, P. J. & Barrett, J. B. Use of a genus- and species-specific multiplex PCR for identification of enterococci. J. Clin. Microbiol. 42, 3558–3565 (2004).

    CAS  Article  Google Scholar 

  49. 49.

    Stankowska, D., Kwinkowski, M. & Kaca, W. Quantification of Proteus mirabilis virulence factors and modulation by acylated homoserine lactones. J. Microbiol. Immunol. Infect. 41, 243–253 (2008).

    CAS  PubMed  Google Scholar 

  50. 50.

    Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).

    CAS  Article  Google Scholar 

  51. 51.

    Kuczynski, J. et al. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr. Protoc. Bioinformatics 36, 10.7.1–10.7.20 (2011).

    Google Scholar 

  52. 52.

    Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).

    CAS  Article  Google Scholar 

  53. 53.

    Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).

    CAS  Article  Google Scholar 

  54. 54.

    Tsuda, A. et al. Influence of proton-pump inhibitors on the luminal microbiota in the gastrointestinal tract. Clin. Transl Gastroenterol. 6, e89 (2015).

    CAS  Article  Google Scholar 

  55. 55.

    Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).

    Article  Google Scholar 

  56. 56.

    Ojiro, K. et al. MyD88-dependent pathway accelerates the liver damage of concanavalin A-induced hepatitis. Biochem. Biophys. Res. Commun. 399, 744–749 (2010).

    CAS  Article  Google Scholar 

  57. 57.

    Hayashi, A. et al. A single strain of Clostridium butyricum induces intestinal IL-10-producing macrophages to suppress acute experimental colitis in mice. Cell Host Microbe 13, 711–722 (2013).

    CAS  Article  Google Scholar 

  58. 58.

    Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016).

    Article  Google Scholar 

  59. 59.

    Brisse, S. et al. wzi Gene sequencing, a rapid method for determination of capsular type for Klebsiella strains. J. Clin. Microbiol. 51, 4073–4078 (2013).

    Article  Google Scholar 

  60. 60.

    Pan, Y. J. et al. Capsular types of Klebsiella pneumoniae revisited by wzc sequencing. PLoS ONE 8, e80670 (2013).

    Article  Google Scholar 

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We thank S. Chiba, S. Shiba, R. Morikawa, T. Katayama, A. Ikura, Y. Mikami and T. Sujino (Division of Gastroenterology and Hepatology, Keio University) for technical assistance and critical reading of this manuscript. This study was supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI Grant-in-Aid (C) 16K09374 and (A) 15H02534, the Advanced Research and Development Programs for Medical Innovation (AMED-CREST; 16gm1010003h0001), the TAKEDA Science Fund, Ezaki Glico Co. Ltd and Keio University Medical Fund. K.H. was funded through AMED LEAP under grant number JP17gm0010003. A. Yoshimura was supported by the JSPS KAKENHI Grant-in-Aid (S) JP17H06175, Challenging Research (P) JP18H05376 and AMED-CREST JP18gm0510019 and JP18gm1110009.

Author information




N.N. and T.K. designed the project. N.N., N.S., R.A., K.M., T.T., Takahiro S., Y.K., P.-S.C., N.T., Akihiro Y., M.K. and H.A. performed the experiments. W.S. and M.H. performed the bacterial sequence, microbiome analyses and contributed to data discussions. K.A., S.N. and K.H. provided essential materials and contributed to data discussions. N.N., N.K., M.S., Akihiko Y., Toshiro S. and T.K. interpreted the experimental data. N.N., N.K. and Toshiro S. wrote the manuscript. T.K. critically revised the manuscript and supervised the study.

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Correspondence to Toshiro Sato or Takanori Kanai.

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Supplementary information

Supplementary Information

Supplementary Figures 1–8.


Reporting Summary

Supplementary Table 1

Demographic characteristics of study subjects.

Supplementary Table 2

Fpkm values in RNA-seq analysis.

Supplementary Table 3

Phylogenetic relationship among K. pneumoniae strains used in this study.

Supplementary Table 4

Genes positively correlated with the epithelial pore-forming capacity.

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Nakamoto, N., Sasaki, N., Aoki, R. et al. Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis. Nat Microbiol 4, 492–503 (2019).

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