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The Microbiota at the Intestinal Mucosa-Immune Interface: A Gateway for Personalized Health


Generating solutions




2012 Large-Scale Applied Research Project Competition – Genomics and Personalized Health

Genome Centre(s)



Project Leader(s)

Fiscal Year Project Launched


Project Description

Goal: To develop a simple, non-invasive and cost-effective approach to detecting IBD and determining its severity, with a view to developing new treatments for the condition.

Inflammatory bowel diseases (IBD), such as Crohn’s disease and ulcerative colitis, are incurable debilitating lifelong diseases that can affect children. Early detection is critical to avoiding complications and improving their quality of life. Now, however, there is no single test to determine the presence or type of IBD and the tests that exist are very uncomfortable for children.

Drs. Alain Stintzi, David Mack and team are developing a simple, non-invasive approach to detecting IBD that will also be more cost effective. Using cutting-edge technology, the scientists will examine intestinal bacteria to develop better ways of identifying IBD and determining its severity. This work could also lead to new treatment, enhancing the quality of life for children everywhere.

Project outcomes*:

  • Identified biomarkers for Inflammatory Bowel Disease (IBD) that can be used to develop non-invasive, diagnostic tools and therapeutic techniques that will potentially accelerate diagnosis, and lead to individualized and more effective treatment. This could reduce current need for repeat colonoscopies and radiological imaging, minimizing the potential for over or undertreatment, reduce complications and thereby improve quality of live and reduce health care costs.
  • Developed biomarkers to better differentiate between Crohn’s Disease and ulcerative colitis with greater accuracy.
  • Built base of biomarkers, data sets, and techniques now being used for further research to develop and validate individualized Crohn’s disease treatments for children, and to broaden treatment strategies to include the microbiome (bacteria in the gut).
  • Submitted four patents, licensed three biomarkers and created a spin-off, Biotagenics, to continue validation efforts and commercialize biomarkers as diagnostic tools for IBD.
  • Published 13 high-impact papers, in journals such as Nature Communications, Gut, Analytical Chemistry, Microbiome and Inflammatory Bowel Diseases, and a review article in Inflammatory Bowel Diseases. This includes three papers from GE3LS component of project.
  • Delivered 76 presentations to local, national, and international expert conferences, including the 2017 World Congress on Pediatric Gastroenterology.
  • Initiated collaboration with the Canadian Children’s Bowel Disease Network, a $5 million funded project through the Children with Intestinal and Liver Diseases (C.H.I.L.D.) Foundation in collaboration with the Canadian Institutes of Health Research.
  • Expanded research network to include new collaborations with research teams across Canada, United States, and France.
  • Attracted new funding for next stage of research into treatments from Genome Canada and Canadian Institutes for Health Research. (See current project: Microbiome-based precision medicine in inflammatory bowel disease)
  • Currently exploring collaborations with Broad Institute and Helmsley Charitable Trust – two prestigious US-based funding organizations with interests in genomics.
  • Brought international recognition to Children’s Hospital of Eastern Ontario (CHEO) Research Institute. Recognized by 2018 external, international peer-review as national leader in research into the microbiome and IBD.
  • Expanded research team to 30 people, including the addition of metabolomics and epidemiology specialists that allowed the laboratory to pursue a multidisciplinary approach, accelerate the rate of discovery, and begin to move new diagnostic approaches closer to use.
  • Trained graduate students and postdoctoral fellows who have gone on to secure faculty positions in universities, as well as Health Canada and the Natural Sciences and Engineering Research Council (NSERC).
  • GE3LS Component: Collaboration with GE3LS researchers in Guelph to publish results of studies with IBD patients and their families, providing insight into children’s perspectives on the daily challenges of living with the disease. This included the ethical and social implications of research participation, decision-making around outcome disclosures, peer interactions, and family food choices in the context of gastrointestinal disorders. These findings will be useful for caregivers, health care providers, researchers, research ethics boards, and others working with IBD youth. Researchers also illustrated the role that microbial genomics can play in developing learning health care systems (LHS) that integrate science, informatics, incentives, and culture for continuous improvement and innovation in health care practices.

*Revised July 2018