Background on the Canadian Microbiome Initiative (CMI)

The human body plays host to trillions of microorganisms, including bacteria, viruses and protists. These microorganisms constitute the "Human Microbiome" that resides both on the surface and deep within numerous sites in our bodies. It is estimated that the number of microbial cells outnumbers host cells by a factor of at least 10:1 and that they encode approximately 100-fold more genetic information than the human genome. It has been recognized that microorganisms play an important role in human health, not just as pathogens, or as benign communities that keep pathogens at bay, but also in association with a number of chronic health conditions including gastrointestinal diseases, obesity, autoimmune diseases, diabetes, cancer, arthritis, asthma and cardiovascular disease. Perturbations in the normal microbiome have also been associated with certain neurological and behavioural changes. Until recently the task of studying the human microbiota was daunting, not only because of the sheer number of organisms colonizing the human body, but also because of the difficulties involved in studying colonies of microorganisms, and the interactions between them in their natural environment. However, with the emergence of the field of metagenomics and the availability of a new generation of genome sequencing platforms, it is now possible to sequence, analyze and characterize complex microbial communities fast and efficiently. These cutting-edge genomic and bioinformatics technologies open the door for biological studies on the complex relationships between microorganisms and humans.

The National Institutes of Health (NIH), through the Human Microbiome Project (HMP), are sequencing and analyzing the genomes of the human microbiome in selected body sites in order to determine whether there is a core set of microbiota shared by all humans. Using this reference database, it is hoped to be able to predict the genetic capabilities of unknown species on the basis of similarities with known genes and to assess the role of the human microflora in health and disease. Much of the sequencing work is being undertaken by the HMP, but the vast amounts of data required calls for a coordinated international approach in which common techniques are used to collect samples, extract DNA and annotate data - hence the recent creation of the International Human Microbiome Consortium (IHMC). IHMC coordinates the microbiome initiatives around the world including those in the EU, China, Japan, Singapore, Australia and Canada.

Canada is well placed to take advantage of these ongoing initiatives due to research strengths in fields of gastroenterology, neuroimmunology, virology and infectious diseases and also our collaborative research culture and publicly-funded health care system. On behalf of CIHR, the Institute of Infections and Immunity (III) has championed the development of a conceptual framework for a Canadian microbiome strategy and engaged Canadian researchers in establishing research strategies and priorities related to the HMP. In September 2007, III initiated the Canadian Microbiome Initiative (CMI) to align with the HMP and to help Canadian researchers take a leading role in the IHMC. In June 2008, III and Genome Canada co-hosted the Canadian Microbiome Workshop, which brought together Canada's leading microbiome researchers to explore and develop strategies and priorities for the CMI and explore the research areas in which Canada can make unique contributions. III has already secured significant funds in support of CMI and developed strong national partnerships to support a strong Canadian presence in the field of microbiome research.

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