CMI Funding Decisions

Researchers funded in the Emerging Team Grant: Canadian Microbiome Initiative competition

1. Project title: Influences of Host Genome on the Human Gut Microbiome: Studies in a Healthy Cohort Carrying Crohn's Disease Risk Alleles

Principal Investigators:

  • Kenneth Croitoru, Mount Sinai Hospital, Toronto
  • Mark S. Silverberg, Mount Sinai Hospital, Toronto


  • Dennis Cvitkovitch, University of Toronto
  • Gabriel Moreno Hagelsieb, Wilfrid Laurier University, Waterloo
  • Andrew Paterson, Hospital for Sick Children, Toronto
  • Wei Xu

Inflammatory bowel disease (IBD) is a condition that causes inflammation and ulcers in the intestine and colon and affects over 200,000 Canadians. Dr. Croitoru and his team are conducting a prospective study of currently healthy people who have an elevated genetic risk of developing Crohn's disease. This study, entitled "The GEM Project", will identify changes in the gut bacteria and host immune response in people who develop IBD, before they develop disease. By assessing these individuals, Dr. Croitoru and his team can study how specific genes influence the makeup of the entire population of gut bacteria in healthy people.

2. Project title: Modeling and mapping microbial diversity and function with marker genes, genomes and metagenomes

Principal Investigators:

  • W. Ford Doolittle, Dalhousie University, Nova Scotia
  • Robert G. Beiko, Dalhousie University, Nova Scotia
  • Joseph Bielawski, Dalhousie University, Nova Scotia
  • Marc Ereshefsky, University of Calgary


  • Olga A. Zhaxybayeva, Darmouth College, Hanover, NH

Dr. Doolittle's team will characterize the bacteria in and on our bodies and assess their role in health and disease. The results will teach us how to encourage the "good" bugs and discourage the "bad". Achieving this goal requires better methods for identifying microbial types and predicting their activities. The team will; develop software for characterizing the diversity and predicting the impact of the many human microbial communities. It is expected that this software will be of wide and immediate use to all microbiome scientists.

3. Project title: Impact of the Microbiota on Immune Development and Disease

Principal Investigators:

  • Barton B. Finlay, University of British Columbia, Vancouver
  • Kelly McNagny, University of British Columbia, Vancouver
  • William W. Mohn, University of British Columbia, Vancouver


  • Tobias Kollmann, University of British Columbia, Vancouver
  • Richard Moore, BC Cancer Agency
  • Kieran O’Doherty, University of British Columbia, Vancouver
  • Stuart E. Turvey, Child & Family Research Institute

Allergic asthma is an ever-increasing problem in developed countries and affects up to 20% of all Canadians. Recent evidence suggests that shifts in the normal microbiota may play a significant role in the development of asthma (the so-called "hygiene hypothesis"). However, the role of the gastrointestinal microbiota in asthma has never been explored experimentally, and no attempt has been made to identify the microbial populations associated with asthma. Dr. Brett Finlay and his team propose to explore the effect of different antibiotics on the microbiota and immune development. This research will provide key information about the role of the intestinal microbiota in immune development and atopic diseases and could lead to new ways of treating asthma.

4. Assessing the breadth and depth of cystic fibrosis-associated polymicrobial respiratory tract infections

Principal Investigators:

  • David Guttman, University of Toronto
  • Leah E. Cowen, University of Toronto
  • Alan R. Davidson, University of Toronto
  • David M. Hwang, University Health Network, Toronto
  • Kieran C. O’Doherty, University of Guelph
  • John Parkinson, Hospital for Sick Children, Toronto
  • Diana E. Tullis, St. Michael’s Hospital, Toronto
  • Valerie J. Waters, Hospital for Sick Children, Toronto
  • Yvonne C. Yau, University of Toronto


  • Heather Maughan

Cystic Fibrosis (CF) is the most common fatal genetic disease among individuals of European descent, with mortality due to respiratory problems associated with repeated episodes of bacterial infection of the airways. Dr. Guttman's team will use state-of-the-art genomic technologies to characterize the composition and dynamics of the microbial communities found in the CF lung during the progression of the disease and the initiation of antibiotic treatment. The long-term goal of the study is to establish guidelines to assist clinicians in the design and selection of therapies tailored for individual patients based on their clinical status and the specific nature of the infectious community.

5. Project Title: Synergy in Microbiota Research (SyMBIOTA)

Principal Investigators:

  • Anita L. Kozyrsky, University of Alberta
  • Allan B. Becker, University of Manitoba
  • David Guttman, University of Toronto
  • Kent T. Hayglass, University of Manitoba
  • Piush Mandhane, CHILD Study
  • James A. Scott, University of Toronto


  • Dean A. Befus, University of Alberta
  • Radha Chari, University of Alberta
  • Catherine J. Field, Catherine J. Field
  • Terry P. Klassen, Manitoba Institute of Child Health
  • Stuart E. Turvey, Child & Family Research Institute

Dr. Kozyrskyj and the SyMBIOTA research team will study the impact of antibiotic use on the composition of intestinal microbiota in newborn infants. The team is exploring whether changes in infant microbiota are associated with the development of allergy and asthma in children. The team will follow 2,500 infants enrolled in the Canadian Healthy Infant Longitudinal Development (CHILD) study to test the association between the use of antibiotics, changes in the infant gut microbiota and the development of atopic disease. Study objectives will be achieved through linkage of detailed data on antibiotic use in infants from provincial prescription database records with clinical data and bacterial profiles of their fecal samples.

6. Project title: The Vaginal Microbiome Project Team

Principal Investigators:

  • Deborah M. Money, University of British Columbia
  • Alan D. Bocking, University of Toronto
  • Sean M. Hemmingsen, National Research Council Canada
  • Janet E. Hill, National Research Council Canada
  • Gregor Reid, Western University


  • Timothy Dumonceaux, Agriculture and Agri-Food Canada
  • Gregory B. Gloor, Western University
  • Matthew G. Links, Agriculture and Agri-Food Canada
  • Kieran O’Doherty, University of Guelph
  • Patrick K. Tang, BC Centre for Disease Control
  • Julianne E. Van Schalkwyk, University of British Columbia
  • Mark H. Yudin, St. Michael’s Hospital, Toronto

Perturbations in the microbial community of the vagina can result in enhanced acquisition of HIV and other sexually transmitted infections, pelvic inflammatory disease, infertility, early pregnancy loss, and localized infections that significantly impact quality of life. To understand the vaginal microorganisms and how they can modulate women's health and diseases, Dr. Deborah Money and her team will examine and identify the microorganisms living in the female genital tract. The data collected will help to identify and characterize microorganisms that are related to womens' health and potentially lead to the development of new treatments and therapies.

7. Project title: Respiratory tract microbiome dynamics and the interplay of commensal bacteria with resident pathogens

Principal Investigators:

  • Michael Surette, McMaster University, Hamilton
  • Dawn Bowdish, McMaster University, Hamilton
  • Anthony Schryvers, University of Calgary
  • Jim Kellner, University of Calgary
  • Jennie Johnstone, McMaster University

In general, the bacteria that live on, or in, the human body are beneficial (commensal bacteria) and are essential for health. However, lurking among the commensal bacteria are pathogens which are commonly found in healthy individuals and are held in check by the commensals. Dr. Mike Surette and his team will study the commensal microbiota in the respiratory tract and investigate how they inhibit or activate the pathogens that cause disease. Understanding these interactions may lead to new ways to control respiratory infections.

Researchers funded in the CIHR-III Microbiome Catalyst Grant competition

Principal Investigator Institution Project Title
Allen-Vercoe, Emma University of Guelph Investigating the potential effects of host-derived stress hormones on the human gut microflora
Dr. Allen-Vercoe is exploring the effects of host-derived stress hormones on the human gut microbiota and to show that these stress hormones exert a direct effect on the population balance of the gut's microflora.
Finlay, Barton University of British Columbia The Role of the Gastrointestinal Microbiota in Asthma
Dr. Finlay is determining whether shifts in resident gastrointestinal microbiota play a role in developing atopic diseases such as asthma (i.e. testing the so-called "hygiene hypothesis).
Holt, Rob BC Cancer Research Centre Linking Infectious Agents to Cancer: A Metagenomics Approach
Dr. Holt is analysing RNA samples from early stage tumours with the intention of determining if an infectious agent is detectable in these neoplasms using a method called Whole Transcriptome Shotgun Sequencing.
Hwang, David University Health Network Assessing the impact of polymicrobial pulmonary infections in cystic fibrosis via metagenomics
Dr. Hwang is trying to show that the lungs of CF patients harbour dozens of bacterial species, and that the composition of the bacterial community in the lung affects the severity of the disease and the effectiveness of different treatments.
Kozyrskyj, Anita University of Alberta The impact of antibiotics on intestinal microbiota of infants
Dr. Kozyrskyj is measuring the effect of antibiotic use during infancy on the composition of intestinal microbiota and whether it is associated with the development of atopic disease in children.
Manges, Amee McGill University Microbial metagenomics of the intestinal microbiota and the etiology of Clostridium difficile-associated disease in hospitalized patients
Dr. Manges is investigating the etiology of C. difficile-associated disease in order to test and compare three alternate models of pathogenesis.
Money, Deborah University of British Columbia Metagenomic characterization of the human vaginal microbiome
Dr. Money is looking to determine whether healthy reproductive-aged women share a core vaginal microbiome, with variations that can be clearly defined and correlated with health and disease.
Neufeld, Josh University of Waterloo Establishing a complete taxonomic baseline for the human microbiome
Dr. Neufeld is comprehensively profiling the phylogenetic diversity of the human gut and oral microbiome by pioneering a newly developed high-throughput sequencing technique and developing novel bioinformatic tools for subsequent data analysis.
O'Doherty, Kieran University of British Columbia Developing Ethical and Regulatory Guidelines for Research on the Human Microbiome and its Applications: Speaking to the Experts and Stakeholders
Dr. O'Doherty is undertaking the challenge of collating and critically analysing the diversity of views and positions on human microbiome research and develop and understanding of how the human microbiome project is likely to shape public understanding of health and the human body.
Rioux, Kevin University of Calgary Characterizing the fecal microbiome and bacteria-derived volatile organic compounds in patients with non-alcoholic fatty liver disease (NAFLD)
Dr. Rioux is examining previously unexplored links between compositional and functional changes in the intestinal microbiota and the pathogenesis of liver disease (NAFLD), possibly identifying novel therapeutic targets in the prevention and management of this disease.
Stintzi, Alain University of Ottawa Role of the gut microbiome in Pediatric Gastrointestinal Illnesses
Dr. Stintzi is performing a comprehensive analysis of the gastrointestinal tract microbiome in children with IBD in order to test the hypothesis that the composition of the gut microbiota is uniquely associated with either Crohn's disease and/or ulcerative colitis.
Surette, Michael University of Calgary Elusive respiratory pathogens in the oropharyngeal flora
Dr. Surette is tracking down the elusive pathogens in the oral cavity and upper respiratory tract that are unidentifiable and are currently escaping detection by conventional clinical microbiology.
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