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Over $15M in funding unveiled for microbiome research


Toronto, ON – Significant new funding will allow seven groups of researchers to investigate the many microorganisms that reside in or on the human body and the role they play in health and disease as well as develop new detection methods and treatment options for several chronic diseases. The funding announcement was made today at the Ontario Science Centre by representatives from the Government of Canada, Canadian Institutes of Health Research (CIHR), Genome British Columbia, Canadian Cystic Fibrosis Foundation (CCFF) and the Crohn’s and Colitis Foundation of Canada (CCFC).

“Genome British Columbia is pleased to be partnering with CIHR on this important initiative and to be able to support two leading BC scientists and their teams in areas of research that will have a significant impact on the health of many of Canadians,” says Dr Alan Winter, president and CEO of Genome British Columbia. “This work will build upon existing technologies and capacity developed over recent years through Genome BC, Genome Canada and CIHR funding and has excellent potential for positive results in the fields of immunological disorders and female reproductive health.”

The federal government is providing over $14 million in funding over five years to support the seven new research teams. As well, $1.4 million in funding is being provided by Genome British Columbia, the Crohn’s and Colitis Foundation of Canada, and the Canadian Cystic Fibrosis Foundation. The research teams are based in British Columbia, Alberta, Ontario and Nova Scotia.

“The CIHR Institute of Infection and Immunity (III) is proud to support our seven research teams from across the country that exemplifies the innovation necessary to address and treat a wide range of conditions,” said Dr Marc Ouellette, scientific director for CIHR. “The goal of this initiative is to discover which microbial communities exist in different parts of the human body and to explore how these communities impact and influence human health or disease.”

The funded projects are as follows:

(1) The Vaginal Microbiome Project Team: Our team of researchers, lead by Dr Deborah Money at the Women’s Health Research Institute, and the University of British Columbia, Dr Janet Hill at the University of Saskatchewan, Dr Sean Hemmingsen at the National Research Council Canada, Dr Gregor Reid at the University of Western Ontario, and Dr Alan Bocking at the University of Toronto with many other collaborators will be conducting pioneering research to define a healthy vagina. This will ultimately lead to the development of novel diagnostic tools and interventions that restore and retain health.

(2) Influences of Host Genome on the Human Gut Microbiome: Studies in a Healthy Cohort Carrying Crohn’s Disease Risk Alleles: Understanding the physiological and genetic bases of inflammatory bowel disease. Dr Ken Croitoru and his team at Toronto’s Mount Sinai Hospital are conducting a prospective study of healthy people genetically at risk of developing Crohn’s disease, which is a type of IBD. The study, funded by the Crohn’s and Colitis Foundation of Canada (CCFC) and termed “The GEM Project,” is designed to help researchers identify a change in the gut bacteria or a change in the immune response in people who develop IBD, before they develop the disease. This may be the only way to identify the triggers that cause the disease and will help lead to new strategies for improved diagnoses and treatments. Dr Croitoru is a scientist at Samuel Lunenfeld Research Institute of Mount Sinai Hospital, and a professor of medicine at the University of Toronto, Division of Gastroenterology.

(3) Modeling and mapping microbial diversity and function with marker genes, genomes and metagenomes: Dr Ford Doolittle, Dalhousie University. The human microbiome project aims to (1) characterize the diversity of types of bacteria in and on our bodies and (2) assess their various roles in health and disease, so that we might (3) learn better how to encourage the good bugs and discourage the bad. Achieving these interrelated goals requires better methods for identifying microbial types and predicting their activities. These must be based on sounder knowledge of underlying ecological and genetic mechanisms and processes. In the theoretical component of our project we will, through modelling and mapping of the ever vaster genomic and metagenomic databases, advance knowledge of mechanisms and processes. In the practical component, we will develop software for characterizing the diversity and predicting the impact of the many microbial communities we humans harbor.

(4) Assessing the breadth and depth of cystic fibrosis-associated polymicrobial respiratory tract infections: Dr David Guttman, University of Toronto. 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. The funding will allow us to use state-of-the-art genomic technologies to characterize the composition and dynamics of the microbial communities (bacterial, fungal, and viral) found in the CF lung during the progression of the disease and the initiation of antibiotic treatment. We will also assess the fine-level population dynamics of two key bacterial and one fungal species commonly associated with clinical exacerbations, study the diversity of metabolic profiles and antibiotic resistance found within these communities, and finally, the examine ethical issues related to the collection of patient data and samples for basic and clinical research. Our long-term goal 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) Impact of the Microbiota on Immune Development and Disease: Dr Stuart Turvey, Dr Richard, Moore, Dr Bill Mohn, Dr Kelly McNagny, Dr Brett Finlay and Dr Tobias Kollmann. There is increasing evidence that intestinal microbiota impact on immune development and disease. Allergic asthma is an ever-increasing problem in developed countries and affects up to 20% of all Canadians. Although there are many theories about the potential cause of asthma, the actual causes remain undefined. Recent evidence suggests that shifts in resident microbiota (normal flora) may play a significant role in atopic diseases such as asthma he so-called “hygiene hypothesis”). However, the role of the astrointestinal microbiota in asthma has not been explored experimentally, and no attempt has been made to identify microbial populations affecting asthma. We propose to assemble a strong interdisciplinary team to explore the contribution of the microbiota to immune development and the atopic disease asthma in both murine and human hosts. We will employ a well-characterized murine model of asthma to determine how the microbiota affects this disease by varying the microbiota using different antibiotics. The murine immune responses will be monitored following these microbiota shifts. Moreover, as part of the CHILD longitudinal cohort study, immune analysis will be performed on samples taken from children from birth until 1 year of age. In correlation with these studies, the composition of the intestinal microbiota will be characterized, and correlated with atopic diseases, as well results from the murine studies. Applied ethical questions associated with these results will also be studied. Collectively, these approaches will provide key information about the role of the intestinal microbiota in immune development and atopic diseases such as asthma.

(6) Synergy in Microbiota Research: Piush Mandhane, Anita Kozyrskyj, Grace Zeng, Dean Befus, David Guttman, James Scott, Brenda Koster, Meghan Azad, and Tedd Konya. Our SyMBIOTA research team will study the impact of antibiotic use in newborn infants on the composition of intestinal microbiota at age 3 months and one year. Changes in infant microbiota will be evaluated for their effe
ct on the development of allergy and asthma in children. This will be a study of 2,500 infants enrolled in the CIHR and AllerGen NCE-funded Canadian Healthy Infant Longitudinal Development (CHILD) study. 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. The composition of the infant’s microbiota will be determined using DNA sequencing techniques. We have assembled an expert team of researchers across five Canadian universities, ranging from microbiologists, epidemiologists to immunologists. The proposed database linkage methods are novel and are being tested at the Winnipeg site of CHILD.

(7) Respiratory tract microbiome dynamics and the interplay of commensal bacteria with resident pathogens: Dr Michael Surette, McMaster University. The bacteria of the airways can be described as the good, the bad and the ugly. Most are good, protecting us from infections. However, there are pathogens present usually kept in check by other members of the community. Dormant pathogens can also be provoked into behaving badly by seemingly good bacteria. Dr Surette is leading a team from McMaster University to define who’s who in this complex community in order to understand how bacteria interact with each other and our immune system. In collaboration with Dr Dawn Bowdish, an assistant professor of pathology and molecular medicine, and Dr Jennie Johnstone, an assistant professor of medicine, (and Professors Tony Schryvers and Jim Kellner from the University of Calgary). Dr Surette is working to shed light on how this bacterial community in the very young and in the elderly makes them more susceptible to respiratory infections.