Analysis of the gut microbiome of Japanese inflammatory bowel disease patients

Abstract Background Gut microbiome dysbiosis has been reported in patients with inflammatory bowel disease (IBD). However, gut microbiome of healthy Japanese individuals differs from that of other populations and gut microbiome of Japanese IBD patients has not been well characterized. We conducted a cross-sectional study to characterize the gut microbiome of Japanese patients with Crohn’s disease (CD) and ulcerative colitis (UC). Methods Two-hundred and eighty-four IBD patients (39 CD patients and 245 UC patients) and 31 healthy participants were enrolled. Gut microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina Miseq. Results Significant differences were observed among the gut microbiome of CD patients, UC patients and healthy individuals. Species richness and evenness were significantly lower in patients with active IBD than in healthy individuals. At the genus level, Bifidobacterium was most abundant genera in all three groups. Pathogenic obligate anaerobes such as Prevotella and Veillonella were increased and commensal bacteria such as Ruminococcus was decreased in IBD patients compared with healthy individuals. Conclusions CD patients and UC patients showed unique patterns of gut microbiome dysbiosis. Patients with active IBD had severe dysbiotic changes. However, characteristic features of the gut microbiome of Japanese individuals, such as high abundance of the genus Bifidobacterium, were maintained in IBD patients.