At Canada’s Food University, microbes are rapidly emerging as a star player in the quest to produce food safely and sustainably, and improve gut health in both food animals and consumers.  This is because microbes – ubiquitous yet virtually invisible to the naked eye – play essential but usually unsung roles across the food chain.  Some of these roles are well known; for example, microbes help cycle nutrients in soil, making them available for crop uptake and growth, and without microorganisms we wouldn’t have some of our favourite foods such as cheese, yoghurt, wine and beer. But other roles are just beginning to be understood, such as the ability of “good” microbes to suppress harmful pathogens in soil, plants, food products and the gut.

Before we can begin to appreciate the power of microbes to influence living systems, it is worth noting just how omnipresent they are.  One teaspoon of soil can hold a billion microbial cells, while the average person is home to more microorganisms than human cells.  The “microbiome” is the term given to the collection of bacteria, viruses, fungi and other microorganisms in a particular environment (such as the soil, gut or whole body).  A good number of microbial species are known to scientists, but the vast majority by far are not – leading many to call the microbiome the next frontier in the life sciences.

Uncovering microbe power

A growing number of researchers from across the University of Guelph campus are united in an effort to uncover how life’s smallest organisms have the power to transform the way we produce food and maintain gut health.  These researchers – from soil scientists and botanists to veterinary pathobiologists and food scientists – are shedding light on the innovative ways that the microbiome can be managed to promote soil, plant, animal and human health. They are aided by exciting new molecular technologies that vastly expand our ability to understand how microbes are connected to each other and their host.  These so-called “omics” technologies (e.g., metagenomics, transcriptomics, proteomics) allow us to see not only what microbes are present, but what genes are being expressed and what proteins and chemicals they are producing.  In the history of science, never before has it been possible to gather this scope and scale of information about the complex communities of microorganisms that play such a dominant role in the living environment.

Dr. Kari Dunfield, a Canada Research Chair and soil scientist in the School of Environmental Sciences, knows first hand how omics technologies have changed the landscape in soil microbiome research.  “Traditional molecular microbial soil ecology focused mainly on the question ‘who is there?’ Now, we are using new technologies to ask instead, ‘what are they doing’?  This allows us to link changes in the composition of microbial communities with changes in ecosystem function.  This in turn is a critical step to understanding how we can adjust our land management practices to improve soil health and productivity.”

But soil is just the first link in a food chain that is heavily influenced by the presence and activity of microbes. Crop plants have their own microbiome, with different microorganisms living within, on and near each plant.  Some of theses microbes can protect their host from plant diseases by producing antimicrobial metabolites, while others produce plant growth hormones or help the plant acquire nutrients.  According to Dr. Manish Raizada, a crop scientist in the Department of Plant Agriculture, one of the most exciting developments in plant microbiome research is the potential to apply beneficial microbes as plant ‘probiotics’ to reduce disease and enhance crop nutrition.  “This is rapidly growing into a multi-billion dollar a year industry,” notes Raizada, who has filed four patents related to microbial inoculants for crops.

At the other end of the food chain are the animals and humans consuming food.  It is increasingly recognized that the gut microbiota of humans and animals is inextricably connected to overall health, but we are only just beginning to understand this link and how it is can be influenced by diet and exposure to pathogens or antimicrobial compounds.  It is an exciting field of study that crosses many departments and colleges at Guelph. In the Department of Animal Biosciences, for example, the lab of Dr. Elijah Kiarie is looking at the impact of feed additives and pathogens on the gut microbial community in poultry, while Dr. Scott Weese in the Ontario Veterinary College is examining how the gut microbiome of domestic animals changes naturally over time, and how it is impacted by the widespread use of antibiotics.

A home away from home

Across the street, the Department of Molecular and Cellular Biology houses a lab where the microbes living in the human gut take centre stage.  Known for her ability to “culture the unculturable”, Dr. Emma Allen-Vercoe has pioneered a system to grow microbes that wouldn’t normally survive outside the depths of the human gastrointestinal tract. Using this innovative “robogut” system, her lab has been a leader in showing how individual human gut microbial species can be linked to wide range of human diseases such as IBD and colon cancer.  The system also led to the development a microbe-based therapeutic that treats C. difficile infections by re-establishing a healthy microbial community in the gut. “C. difficile is an opportunistic pathogen that can cause very serious illness in patients whose gut microbiome has been disrupted by antibiotics or chemotherapy,” explains Allen-Vercoe. “Our microbial treatment offers an alternative to fecal transplants that is safer and more acceptable to patients.”  It is work that has helped to set the stage for a new era in medical research through manipulation of the microbiota to treat disease.

Meanwhile, researchers in food science are figuring out how healthy gut bacteria may be influenced by food processing.  “Processing conditions can influence the survival of probiotics and food pathogens in different ways” notes Dr. Gisele LaPointe, who holds the Dairy Farmers of Ontario Industrial Research Chair.  Her lab is also discovering some of the mechanisms that shape the interactions between “good” and “bad” gut microbes. For example, they have shown that dairy products fermented by some probiotic bacteria are able to reduce the ability of E. coli and Salmonella to invade intestinal cells, thereby minimizing their ability to cause disease. Such work is delivering valuable insights into developing food products that can promote health by modulating the gut microbiome.

In the same department, Dr. Jeff Farber, Director of the Canadian Research Institute for Food Safety, is initiating a project to develop a global food microbiome database to help the scientific community identify novel microorganisms or their metabolites that can be used to inhibit or inactivate pathogens in food such as Listeria or Cronobacter.  He is also working with microbiome researchers across campus to discover novel inhibitors of foodborne pathogens from non-food sources of microorganisms.  “We will be tapping into the enormous potential of the human gut, animal gut, plant and food microbiomes to identify microbes or their metabolites that can help prevent the devastating impacts of foodborne illness, something that affects 4 million Canadians every year,” says Farber.

It is an exciting time for microbiome research globally, and Guelph’s distinct combination of research strength in microbiology, agriculture, plant science and food science is certain to play a major role in unleashing the full potential of microbes to contribute to healthier food systems and consumers.

For more information about these and other microbiome-related research projects at the University of Guelph, contact:

Allen-Vercoe, Emma – Molecular and Cellular Biology

Farber, Jeff – Food Science

Lapointe, Gisele – Food Science

Warriner, Keith – Food Science

Raizada, Manish – Plant Agriculture

Dunfield, Kari – School of Environmental Sciences

Habash, Marc – School of Environmental Sciences

Weese, Scott – Pathobiology

McCann, Kevin – Integrative Biology

Kiarie, Elijah – Animal Bioscience

Janet MacInnes –  Pathobiology

Peter Kim – Mathematics and Statistics