Assessing the colonic microbiota in children: effects of sample site and bowel preparation

Abstract

Objectives Inflammatory bowel disease (IBD) states are associated with gastrointestinal dysbiosis. Mucosal biopsy sampling, retrieving the bacterial community that most directly interacts with the host, is an invasive procedure, and we hypothesize may be sufficiently approximated by other sampling methods. We investigate the relatedness of samples obtained by different methods and the effects of bowel preparation on the gastrointestinal community in a paediatric population. Methods We recruited a cohort of patients undergoing colonoscopy, collecting serial samples via differing methods (rectal swabs, biopsies and faecal matter/luminal contents) pre-bowel preparation, during colonoscopy and post-colonoscopy. Next generation sequencing was used to determine the structure of the microbial community. Results The microbial community in luminal contents collected during colonoscopy was found to be more similar to that of mucosal biopsies than rectal swabs. Community traits of the mucosal biopsies could be used to segregate IBD patients from other patients, and the similarity of the communities in the luminal contents was sufficient for the segregation to be reproduced. Microbial communities sampled by rectal swabs and pre-bowel preparation faeces were less similar to mucosal biopsies. Bowel preparation was found to have no significant long term effects on the microbial community, despite the transient effects evident during colonoscopy. Conclusions A clinically relevant description of the mucosal microbial community can be obtained via the non-invasive collection of luminal contents after bowel cleansing. Bowel preparation in a paediatric population results in no consistent sustained alterations to the gastrointestinal microbiota.