# Comparison of microbiota profiles of fecal samples, rectal swabs and mucosal biopsies in patients with inflammatory bowel disease

## TL;DR

This study compares gut microbiota profiles from different sample types in IBD patients and finds that each sample type has distinct microbial patterns.

## Contribution

The study demonstrates that fecal, rectal swab, and biopsy samples from IBD patients have non-interchangeable microbiota profiles.

## Key findings

- Fecal and rectal swab samples show higher microbial diversity and abundance compared to colonic biopsies.
- Microbiota profiles from different sample types within the same individual are significantly dissimilar.
- Biopsies from the same or different colon locations show similar microbiota profiles.

## Abstract

Gut microbiota changes are associated with inflammatory bowel disease (IBD). In most microbiota studies, intestinal microbiota composition is examined in fecal samples, but their representativeness of mucosa-associated microbiota at inflammation sites remains unclear. This study aimed to explore microbiota composition in different IBD sample types and assess their interchangeability for research and clinical use. Multicentre, prospective, observational study including 200 IBD patients (518 samples). We compared microbiota profiles from faeces, rectal swabs and mucosal biopsies from different colon sites. Microbiota composition was analyzed by Molecular Culture™, a bacterial profiling technique based on species-specific differences in the 16S-23S interspace region of bacterial ribosomal DNA, with taxonomic classification by phylum-specific fluorescent PCR primers. Fecal samples and rectal swabs contained a higher microbial diversity and abundance than colonic biopsies. Microbiota compositions of different sample types within an individual happened to be quite dissimilar (median cosine similarities 0.43–0.53). Within individuals, biopsies from the same location in the colon were just as similar as biopsies from different locations (median cosine similarities 0.85 vs. 0.82, respectively). Fecal samples, rectal swabs and colonic biopsies of an individual show distinct microbiota profiles and should not be used interchangeably in microbiota studies or clinical applications.