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

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.