The mucosal–luminal interface: an ideal sample to study the mucosa-associated microbiota and the intestinal microbial biogeography

Background Alterations in gastrointestinal microbial communities have been linked to human disease. Most studies use fecal samples as a proxy for the intestinal microbiota; however, the fecal microbiome is not fully representative of the mucosa-associated microbiota at the site of disease. While mucosal biopsies can be used instead, they often contain a high proportion of host DNA that can confound 16S ribosomal RNA (rRNA) gene sequencing studies. Methods To overcome these limitations, we sampled the mucosal–luminal interface (MLI) to study the mucosa-associated microbiota. We also employed a simple bioinformatics workflow to remove contaminants from 16S rRNA gene profiling results. Results Our results indicate that the microbial differences between individuals are greater than those between different microenvironments within the same individual. Moreover, biopsy samples frequently contained contaminants that could significantly impact biopsy profiling results. Conclusions Our findings highlight the utility of collecting MLI aspirates to complement biopsies and stools for characterizing human microbial communities.