Microbiome and its relevance to indigenous inflammatory bowel diseases in China

•In this study, 16S full-length rRNA sequencing technology was used to analyze the microbiomics, and the relationship between Shigella flexneri / Shigella sonnei and Chinese IBD patients was first observed.•The result of correlation analysis showed that, although there was a connection in the distribution of the flora, the oral and intestinal flora in Chinese IBD patients were completely different groups.•The study results from Crohn's disease (CD) and ulcerative colitis (UC) showed that, more red meat intake and increased Clostridium was present in CD patients, whereas the increased Ruminococcus was found in patients with UC.•Clinical test showed that the elevated inflammatory markers, impaired liver and kidney function, and dyslipidaemia were present in Chinese IBD patients. Some of the clinical indicators were also associated with Shigella infection. Inflammatory Bowel Disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract with an unknown etiology. Although dysbiosis is implicated in its pathogenesis, deep sequencing and oral microbiota study in Chinese IBD patients is absent. To explore the role of oral / intestinal microbiota in patients with IBD and the potential associations therein. Clinical data, fecal and saliva samples were harvested from 80 patients with IBD (Crohn's disease, CD, n = 69; Ulcerative colitis, UC, n = 11) and 24 normal controls. Microbiomics (16S rRNA sequencing and 16S rRNA full-length sequencing) were used to detect and analyze the difference between IBD patients and normal control. Compared with normal controls, a higher abundance of the intestinal Shigella spp. (Shigella flexneri and Shigella sonnei, which were positively relate to the severity of IBD), lower abundance of intestinal probiotics (Prevotella, Faecalibacterium and Roseburia), and higher abundance of oral Neisseria were present in IBD patients with microbiome. The higher inflammation-related markers, impaired hepatic and renal function, and dyslipidaemia were present in patients with IBD. A higher intake of red meat and increased abundance of Clostridium in the gut were found in CD patients, while the elevated abundance of Ruminococcus in the gut was showed in UC ones. The bacterial composition of saliva and fecal samples was completely different, yet there was some correlation in the distribution of dominant probiotics. Enteric dysbacteriosis and the infections of pathogenic bacteria (Shigella) may associate with the occurrence or developme