Basic Science Article | Published:

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

Pediatric Research (2019) | Download Citation




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.


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.


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.


Our findings highlight the utility of collecting MLI aspirates to complement biopsies and stools for characterizing human microbial communities.

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We thank Ruth Singleton and Amanda Mack for their assistance in collecting patient clinical data and samples. This work was funded by Genome Canada and the Ontario Genomics Institute (OGI-067), CIHR (GPH-129340, MOP-114872, ECD-144627), and the Ontario Ministry of Economic Development and Innovation (REG1-4450). D.M. and A.S. acknowledge funding from the IBD Foundation of Canada, Crohn’s and Colitis Canada, the CHEO foundation, the CHEO Research Institute. and the University of Ottawa Faculty of Medicine. W.M. acknowledges funding from Mansoura University, Egypt. T.A. was supported by a scholarship from King Abdulaziz University, through the Saudi Arabian Cultural Bureau in Canada. J.B. is the recipient of a CIHR/CAG Postdoctoral Award. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Author contributions

W.M., D.M., and A.S. designed the study. D.M. collected the samples. W.M., J.L., T.A., J.M., and J.B. performed the experiments. W.M., J.B., and A.S. analyzed the data. W.M., J.B., and A.S. wrote the manuscript. D.M. and A.S. contributed equally to the work. All the authors contributed to editing and revising the manuscript.

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Author notes

  1. These authors contributed equally: Walid Mottawea, James Butcher


  1. Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada

    • Walid Mottawea
    • , James Butcher
    • , Jennifer Li
    • , Turki Abujamel
    • , Juliana Manoogian
    •  & Alain Stintzi
  2. Childrenʼs Hospital of Eastern Ontario (CHEO) Research Institute, University of Ottawa, Ottawa, ON, Canada

    • David Mack


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Competing interests

A.S. and D.M. co-founded Biotagenics, a clinical microbiomics company. The other authors declare no competing interests.

Corresponding author

Correspondence to Alain Stintzi.

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