Metabarcoding of colonic cleansing fluid reveals unique bacterial members of mucosal microbiota associated with Inflammatory Bowel Disease

Abstract

Background

Inflammatory Bowel Disease (IBD) is a group of chronic idiopathic inflammatory diseases of the gastrointestinal (GI) tract associated with the dysbiosis of gut microbiota. Metabarcoding-based profiling of the gut microbiota of IBD patients is generally based on the stool samples collected from individual patients which rarely represent the mucosa-associated microbiota. The ideal sampling strategy for routine monitoring of the mucosal component of IBD has yet to be determined.

Methods

We hereby compare the microbiota composition of the colonic cleansing fluid (CCF) collected during colonoscopy with stool samples from IBD patients. The relationship between IBD and gut microbiota was revealed through the application of the 16S rRNA amplicon sequencing-based metabarcoding approach. CCF and stool samples were collected from IBD patients with Crohn’s disease and ulcerative colitis.

Results

The present study shows significant differences in the microbial composition of CCF samples, presumably indicating changes in the mucosal microbiota of IBD patients as compared to the control group. Short-chain fatty acid-producing bacteria under the family Lachnospiraceae, the actinobacterial genus Bifidobacterium, the proteobacterial Sutterella and Raoultella are found to contribute to the microbial dysbiosis of the mucosal flora in IBD patients.

Conclusions

CCF microbiota has the capacity to distinguish IBD patients from healthy controls and, thus, may constitute an alternative analysis strategy for the early diagnosis and disease progression in IBD biomarker research.

Keywords:

• 16S rRNA metabarcoding
• inflammatory bowel disease
• gut microbiota
• colonic cleansing fluid
• metagenomics

Disclosure statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Additional information

Funding

This study was supported by Scientific Research Projects of Istanbul University under the projects, Nr. 26934.