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.

Background The bioactivities of commensal duodenal microbiota greatly influence the biofunction of hosts. We investigated the role of Helicobacter pylori infection in extra-gastroduodenal diseases by determining the impact of H. pylori infection on the duodenal microbiota. We sequenced 16S rRNA genes in samples aspirated from the descending duodenum of 47 (male, 20; female, 27) individuals who were screened for gastric cancer. Samples were analysed using 16S rRNA gene amplicon sequencing, and the LEFSe and Kyoto Encyclopaedia of Genes and Genomes methods were used to determine whether the duodenal microflora and microbial biofunctions were affected using H. pylori infection. Results Thirteen and 34 participants tested positive and negative for H. pylori, respectively. We identified 1,404 bacterial operational taxonomic units from 23 phyla and 253 genera. H. pylori infection increased the relative mean abundance of Proteobacteria and Neisseria and decreased the abundance of the two other phyla (Actinobacteria and TM7) and nine genera (Rothia, TM7-3, Leptotrichia, Lachnospiraceae, Megasphaera, F16, Moryella, Filifactor, and Paludibacter). Microbiota features were significantly influenced in H. pylori-positive participants by 12 taxa mostly classified as Gammaproteobacteria. Microbial functional annotation revealed that H. pylori significantly affected 12 microbial metabolic pathways. Conclusions H. pylori disrupted normal bacterial communities in the duodenum and changed the biofunctions of commensal microbiota primarily by upregulating specific metabolic pathways. Such upregulation may be involved in the onset of diseases associated with H. pylori infection.