TH1 cell-inducing Escherichia coli strain identified from the small intestinal mucosa of patients with Crohn’s disease

Shiho Nagayama ,Yuko Kiridooshi,Koji Atarashi,Tomonori Yano,Keijiro Sunada,Takaaki Kawaguchi,Seiko Narushima,Mariko Sekiya,Hironori Yamamoto,Kouichi Miura,Masahira Hattori,Takeshi Tanoue,Atsushi Shiota,Hirotsugu Sakamoto,Kayoko Sugita,Satoru Morita,Yasutoshi Kobayashi,Wataru Suda,Jun Isayama,Nicolas Barnich,Kenya Honda

doi:10.1080/19490976.2020.1788898

Abstract

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.

Highlights

Crohn’s disease (CD) is a debilitating chronic gas trointestinal disease primarily affecting the ileum and colon and is characterized by longitudinal ulcers, aphthae, and stenosis, which are distinct from the characteristics of ulcerative colitis
We examined the small intestinal (SI) juice aspirated before collection of mucosal specimens and found that operational taxonomic units (OTUs) related to E. coli and R. gnavus were less abundant in the juice as compared with mucosal samples (Figure 2d)
We obtained SI samples from patients with CD using the double-balloon endoscopy (DBE) method, which allows for thorough inspection and bacterial isolation from distal and proximal SI unlike standard ileo-colonoscopy

Summary

Introduction

Crohn’s disease (CD) is a debilitating chronic gas trointestinal disease primarily affecting the ileum and colon and is characterized by longitudinal ulcers, aphthae, and stenosis, which are distinct from the characteristics of ulcerative colitis. Genome-wide association studies have revealed more than 100 CD-associated genes, including those encoding NOD2, IL23R, ATG16L1, and TNFSF15.1-3 In addition to host intrinsic factors, extrinsic factors including the gut microbiota are potentially involved in the pathogenesis of CD. The gut microbiota is a potent regulator of host immunity and is reportedly associated with several diseases.[4,5] Increasing evidence indicates that alteration of the microbiota (called microbiota dys biosis) affects CD pathogenesis. A reduction of the α-diversity of the microbiota and a reduced abundance of Faecalibacterium prausnitzii have been frequently reported in the feces of patients with CD.[6] numerous studies have focused on the fecal micro biota, limited information is available regarding small intestinal (SI) mucosal microbiota, which is highly likely to influence CD pathogenesis

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