Bacterial microbiome profiles of the inflamed terminal ileum mucosa in active Crohn's disease patients.

Background: The dysbiosis of the intestinal microbiome relates to the pathogenesis of Crohn's disease (CD). Previous studies have focused on microbiota diversity and composition in CD patients in comparison with healthy individuals. Nonetheless, intestinal flora varies greatly among individuals. This study aimed to characterize the bacterial microbiome profiles of inflamed mucosa in comparison with those of noninflamed mucosa from Crohn's disease patients.

Methods: Sequencing of 16S rDNA V4 was used to identify the bacterial microbiome profiles of twelve pairs of inflamed and noninflamed mucosa from active CD patients.

Results: A total of 753 OTUs were specific to inflamed tissues. Alpha diversity demonstrated that the biodiversity of the bacterial microbiota in the inflamed mucosa was increased, but it was not significantly different from that in the noninflamed mucosa. Linear discriminant analysis effect size (LEfSe) Clustergram showed Micrococcaceae, Bifidobacteriaceae, Bifidobacteriales, Flavobacteriaceae, and Methylobacteriaceae as microbes that were significantly different in the inflamed mucosa of active CD patients. Wilcox test results of genus differences indicated Methylobacterium, Rothia, Shinella, Capnocytophaga, Actinomyces, Gardnerella, Leucobacter, and Bifidobacterium as significantly upregulated genera in the inflamed mucosa of active CD patients compared with their noninflamed mucosa. These findings provide new evidence that the dysbiosis of mucosa-associated microbiota contributes to CD development, from a self-comparison perspective.