Bacteriophages and plasmids in Streptococcus thermophilus

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The dairy industry is a significant part of our heritage and our economy. It is the third largest sector of the Canadian agri-food economy behind grains and red meats. In 2016 (last year for which data are available), dairy farming generated $6.2 billion and manufactured shipments of milk and dairy products equaled $17.7 billion. Overall, the dairy industry accounted for 15.8% of all processing sales in our nation's food and beverage sector. The dairy workforce includes 18,805 dairy farm operators while the manufacturing sector includes 22,904 jobs which are spread into the 471 Canadian dairy factories. Canada produces more than 1,050 cheeses that are listed in the Canadian Cheese Directory. Last year, Mozzarella and pizza cheeses were produced at a record level in Canada (> 148,000 kg, +2.0% from the previous year). A record level was also observed with the production of speciality cheeses (> 163,000 kg, +5.5% from the previous year). There is no indication that this production trend will change. However, our dairy industry faces intense competition in national and international markets and must deliver high-quality products. Cheese manufacture requires the inoculation of milk with carefully selected bacterial cells (starter culture) to properly control the fermentation and to obtain high-quality products. The starter culture is a combination of lactic acid-producing bacteria, from which Streptococcus thermophilus is one of the most important species. It is well documented that increased productivity within existing manufacturing facilities will lead to milk fermentation failures due to bacterial viruses (phages) that destroy the starter cultures. A shut down of production may even be required to thoroughly clean up the facilities. This natural phenomenon leads to low quality products and economic losses. Thus, constant phage monitoring and stringent application of phage control measures are indispensable. One of the key measures is to use phage-resistant bacterial cultures. CRISPR-Cas systems are by far the most important phage defense mechanisms in S. thermophilus and CRISPR-phage-resistant S. thermophilus strains are now used worldwide. However, phages are evolving and they have found ways to bypass the CRISPR-Cas defense systems. This fundamental research program on S. thermophilus will focus on three areas: 1) Phage biology, 2) Phage resistance, and 3) Plasmid biology. This grant will also train several students in various areas of biological sciences such as microbiology, virology, biochemistry, molecular biology, bioinformatics, and food sciences. This ambitious and state-of-the-art program will lead to the most comprehensive analysis of phage-host interactions in a Gram-positive bacterium. This research will provide fundamental knowledge to our Canadian dairy industry to give them a competitive edge. This knowledge will also be applicable to other bacterial strains susceptible to phage attack in industrial fermentations.