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CBS Prof Member of New Human Microbe Project

Scientist grows gut bugs - including novel strains - for global project to learn about human health and disease


Your body is home to trillions of microbes, mostly good or benign, a few bad. Mapping the DNA of those bugs and learning how they affect health is the ambitious goal of new national and international science projects. And a key part of the venture — learning about the gut microbes that enable you to live from one meal to the next — involves a U of G microbiologist.

Prof. Emma Allen-Vercoe, Molecular and Cellular Biology, is the only Guelph member of the Canadian Microbiome Initiative (CMI). Already this year, her lab has provided about 60 strains of gut microbes to the project for DNA sequencing. And with equipment and expertise in her science complex lab, she hopes to grow and provide most of the roughly 1,000 species of gastrointestinal bugs for the initiative, launched this year.

Allen-Vercoe likens the bacterial sequencing project to the Human Genome Project, which saw researchers sequence the three billion chemical base pairs that make up our DNA. Funded this year by the Canadian Institutes of Health Research (CIHR) and Genome Canada, the CMI will allow researchers in this country to help sequence bacterial DNA and develop techniques to learn about microbes' role in health and disease.

Despite our intimate relationship with those trillions of bacteria, especially the ones that aid in food digestion and nutrient absorption, we know little about what they are and how they work. That knowledge is critical for diagnosing and treating disease, prescribing antibiotics and developing foods designed for gut health, says Allen-Vercoe, who studies the role of gut microflora in inflammatory bowel disease. Her work is supported by the Crohn's and Colitis Foundation of Canada.

Besides her regular research projects, she is growing representative species from the human gut — some of them never described before — and preparing them for sequence analysis for the Human Microbiome Project. That's an international effort involving researchers in North America, Europe, Asia and Australia cataloguing microbes in and on the human body. The Canadian component — the CMI — involves scientists at universities and research institutions across the country.

“I'm the only person providing gut samples from Canada,” she says.

She's already grown and shipped DNA from strains of about 30 bacterial species to the Broad Institute run by Harvard University and the Massachusetts Institute of Technology. There, researchers sequence the material to gain clues about disease and to apply genomics to medicine. At least one of her strains has been sequenced and made publicly available.

Allen-Vercoe's work involves more than merely growing colonies in an agar-filled Petri dish. Many of these bacteria will grow only in the oxygen-free environment of the gastrointestinal tract. To mimic normal surroundings for these microbes, she has set up a “Robo-gut,” a mechanical apparatus whose computer-controlled array of flasks and tubes will work like a mechanical GI tract. She's preparing that device for operation in a joint research lab in the science complex.

Dr. Bhagirath Singh, scientific director of the CIHR Institute of Infection and Immunity at the University of Western Ontario and leader of the CMI, says 80 to 90 per cent of the microbes in the body are unknown. “We live with them, but we don't know their role.” He says work like Allen-Vercoe's on the “pool of bugs” that live with humans will help in understanding and treating diseases and developing probiotic foods.