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Nagayama M, Yano T, Atarashi K, Tanoue T, Sekiya M, Kobayashi Y, Sakamoto H, Miura K, Sunada K, Kawaguchi T, Morita S, Sugita K, Narushima S, Barnich N, Isayama J, Kiridooshi Y, Shiota A, Suda W, Hattori M, Yamamoto H, Honda K. TH1 cell-inducing Escherichia coli strain identified from the small intestinal mucosa of patients with Crohn's disease. Gut Microbes 2020; 12:1788898. [PMID: 32691669 PMCID: PMC7524366 DOI: 10.1080/19490976.2020.1788898] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Dysbiotic microbiota contributes to the pathogenesis of Crohn's disease (CD) by regulating the immune system. Although pro-inflammatory microbes are probably enriched in the small intestinal (SI) mucosa, most studies have focused on fecal microbiota. This study aimed to examine jejunal and ileal mucosal specimens from patients with CD via double-balloon enteroscopy. Comparative microbiome analysis revealed that the microbiota composition of CD SI mucosa differs from that of non-CD controls, with an increased population of several families, including Enterobacteriaceae, Ruminococcaceae, and Bacteroidaceae. Upon anaerobic culturing of the CD SI mucosa, 80 bacterial strains were isolated, from which 9 strains representing 9 distinct species (Escherichia coli, Ruminococcus gnavus, Klebsiella pneumoniae, Erysipelatoclostridium ramosum, Bacteroides dorei, B. fragilis, B. uniformis, Parabacteroides distasonis, and Streptococcus pasteurianus) were selected on the basis of their significant association with CD. The colonization of germ-free (GF) mice with the 9 strains enhanced the accumulation of TH1 cells and, to a lesser extent, TH17 cells in the intestine, among which an E. coli strain displayed high potential to induce TH1 cells and intestinal inflammation in a strain-specific manner. The present results indicate that the CD SI mucosa harbors unique pro-inflammatory microbiota, including TH1 cell-inducing E. coli, which could be a potential therapeutic target.
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Affiliation(s)
- Manabu Nagayama
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, Tochigi, Japan,Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan,Laboratory for Gut Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomonori Yano
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, Tochigi, Japan
| | - Koji Atarashi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan,Laboratory for Gut Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan,JSR-Keio University Medical and Chemical Innovation Center, Tokyo, Japan
| | - Takeshi Tanoue
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan,Laboratory for Gut Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mariko Sekiya
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, Tochigi, Japan
| | - Yasutoshi Kobayashi
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, Tochigi, Japan
| | - Hirotsugu Sakamoto
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, Tochigi, Japan
| | - Kouichi Miura
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, Tochigi, Japan
| | - Keijiro Sunada
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, Tochigi, Japan
| | - Takaaki Kawaguchi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan,Laboratory for Gut Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Satoru Morita
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Kayoko Sugita
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Seiko Narushima
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan,Laboratory for Gut Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Nicolas Barnich
- UMR 1071 Inserm/Université Clermont Auvergne; USC-INRA 2018, Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), CRNH Auvergne, Clermont-Ferrand, France
| | - Jun Isayama
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan,JSR-Keio University Medical and Chemical Innovation Center, Tokyo, Japan
| | - Yuko Kiridooshi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan,JSR-Keio University Medical and Chemical Innovation Center, Tokyo, Japan
| | - Atsushi Shiota
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan,JSR-Keio University Medical and Chemical Innovation Center, Tokyo, Japan
| | - Wataru Suda
- Laboratory for Gut Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan,Cooperative Major in Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Masahira Hattori
- Laboratory for Gut Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan,Cooperative Major in Advanced Health Science, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hironori Yamamoto
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, Tochigi, Japan
| | - Kenya Honda
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan,Laboratory for Gut Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan,JSR-Keio University Medical and Chemical Innovation Center, Tokyo, Japan,CONTACT Kenya Honda Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
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