Mucosa-Luminal Interface: A Highly Valuable Sample to Study the Mucosa-Associated Microbiota and the Intestinal Microbial Biogeography

Background: Alterations in the microbial communities that reside within the gastrointestinal tract have been linked to human disease. However, many studies use fecal samples as a proxy of the intestinal microbiota. This represents a major challenge for understanding the mechanistic role of the intestinal microbiota in disease as the fecal microbiome is not fully representative of the mucosa-associated microbiota at the site of disease. The primary sample source for profiling mucosa-associated microbiota are mucosal biopsies. Unfortunately, biopsies contain a high proportion of contaminating host DNA as compared to microbial DNA and these conditions have been shown to confound the interpretation of results from 16S-rRNA gene sequencing studies. Alternative sample sources that overcome these obstacles would be useful for the field.Results: We sampled the mucosa-luminal interface (MLI) to study the mucosa-associated microbiota and enhance the results obtained from biopsy and stool samples. We employed a simple bioinformatics workflow to remove contaminants from the results of 16S rRNA gene-based microbial profiling and demonstrate that contaminants may significantly impact the results of studies using intestinal biopsies as their biological samples. Our results indicate that the microbial differences between individuals are greater than the differences between the different microbial microenvironments within the same individual. However the microbial communities within the MLI, biopsy and stool samples are each enriched for distinct functional capacities.Conclusions: Our collective findings reveal the utility of collecting MLI aspirates to complement biopsies and stools as for characterizing human microbial communities. In particular MLI aspirates can mimic the regional specificity of biopsies, while still providing comparable biomass as compared to stools. The latter characteristic is important for avoiding technical contaminants and for potentially performing multiple meta-omic studies on the same sample. Moreover, MLI samples represent an important sample type in their own right to characterize human microbiota communities. Only by combining all three sample types will we achieve a complete picture of the human colonic microbiome, from strongly adherent mucosal communities (biopsies) to the more loosely mucosa-associated (MLI) and luminal (stool) microbiota.