Speakers – June 1, 2022 – Concurrent 1A

Genomics: Applications in Food Science

Dr. Lawrence Goodridge, Leung Family Professor of Food Safety, Director, Canadian Research Institute for Food Safety – Ontario Agricultural College

After completing a B.Sc. Honours degree in Microbiology at the University of Guelph, Lawrence completed both his M.Sc. and Ph.D. degrees in Food Science with an emphasis on microbial detection of foodborne pathogens, also at Guelph, before leaving for a Postdoctoral Fellowship to continue his training in microbial food safety in the laboratory of Dr. Michael Doyle in the Center for Food Safety at the University of Georgia. Prior to returning to Guelph, Lawrence has held faculty positions at the University of Wyoming and Colorado State University. More recently, he was the Ian and Jayne Munro Chair in Food Safety in the Food Science Department at McGill University. In January, 2019, Lawrence joined the Department of Food Science as Director of the Canadian Research Institute for Food Safety, where he holds the Leung Family Professorship in Food Safety.  Dr. Goodridge conducts research related to control and detection of pathogenic microorganisms including bacteria, viruses and parasites. Dr. Goodridge has published more than 100 peer reviewed journal articles and book chapters, and has been awarded more than $30 million in research funding from US, Canadian and international funding sources.


Genomics: Applications in Food Science session

Genomic approaches continue to transform the way we produce food. As the field of genomics continues to change rapidly, there is a need for ongoing genomics sessions at conferences to allow attendees to keep up to date with the new advancements in genomics as it applies to food science. Some recent examples of the use of genomics in food science include optimizing food production in the context of climate change (i.e. producing drought resistant crops or livestock that are less resistant to disease), production of new foods and food based products (lab grown meat, plant based meat), increasing food safety (detecting outbreaks faster), and decreasing food spoilage and waste.

In the Genomics: Applications in Food Science session, conference attendees will learn about genomics, beginning with an overview of the history and terminology of genomics, as well as advanced genome analytical methods such as whole genome sequencing, metagenomics, and bioinformatics analysis. Participants will also gain an understanding of how genomics can be used to characterize food-fermenting lactic acid bacteria, and how genomics is being used to reduce the need for antibiotic use in milk production.

Dr. Michael Gänzle, Professor and Canada Research Chair in Food Microbiology and Probiotics (Tier I) – University of Alberta

Dr. Gänzle’s research aims to link microbial physiology and ecology to food quality and host health. His research interests include the development of novel non-thermal technologies for food preservation, aiming to understand mechanisms of bacterial resistance to pathogen intervention technologies, and the functional characterisation of lactic acid bacteria for use as starter cultures or probiotics in food and agricultural applications with a focus on cereal fermentations. Dr. Gänzle was recognized as a Clarivate “highly cited researcher” in 2021, serves as Associate Editor of “Frontiers in Microbiology” and is member of the editorial board of “Food Microbiology”, “Applied and Environmental Microbiology”, and the “International Journal of Food Microbiology”.


Discovery of evolution, ecology and physiology of food-fermenting lactic acid bacteria by comparative genomics

Discovery of evolution, ecology and physiology of food-fermenting lactic acid bacteria by comparative genomics Michael G. Gänzle1, Fuyong Li2, Jens Walter3, and Jinshui Zheng4 1)University of Alberta, Dept. of Agricultural, Food and Nutritional Science 2)City University of Hong Kong, Department of Infectious Diseases and Public Health 3)University College Cork, School of Microbiology and Department of Medicine 4) Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology Introduction. Organisms in the family Lactobacillaceae include most food fermenting lactic acid bacteria; conversely, most species in the Lactobacillaceae occur in food as fermentation organisms or as spoilage organisms. Genome sequence data has become available for most type strains in the Lactobacillaceae in 2015; to date, genome sequences have become available for virtually all of the 358 validly published species in the family. Comparative genomic analyses that are enabled by these sequence data provide an unprecedented tool for discovery of evolution, ecology, and physiology of lactic acid bacteria. Evolution. Phylogenetic analysis with single core genes reliably identified the phylogenetic clades that are now recognized as genera but did not provide sufficient resolution to determine the relationships of these clades to each other. Core genome phylogeny at the family level demonstrated that heterofermentative lactic acid bacteria are monophyletic and evolved from a common ancestor, indicating that the switch from homofermentation to heterofermentation was a singular event. At the species level, analysis of Limosilactobacillus reuteri revealed that the species has evolved from a rodent-associated ancestor to 10 phylogenetic lineages, four of these remained associated with rodents but others switched their hosts to adapt to birds, non-human primates, herbivores or swine. Host switches were associated with substantial changes in the accessory genomes, and resulted in the loss of the ability to colonize mice. Ecology. Lactobacilli have been studied for more than a century but most of these studies per conducted with the perspective of their relevance in food or as probiotic organisms. Genome sequence data in combination with the ability to mine large scale metagenomic datasets demonstrated that lactobacilli can be differentiated into vertebrate host adapted organism, insect adapted organism, nomadic organisms and free-living or plant associated organisms. This differentiation enabled the identification of lifestyle-specific traits, e.g. acid resistance mechanisms for vertebrate host adapted lactobacilli and antimicrobial resistance for nomadic organisms, and facilitates the selection of organisms for specific applications. Physiology. Many of the physiological traits that are relevant for applications as food and feed starter cultures or as probiotics are shared by most strains in a genus; examples include exopolysaccharide formation by extracellular glycosyl hydrolases in the genera Limosilactobacillus and Liquorilactobacillus, and the conversion of lactate to acetate 1,2 propanediol in the genera Levilactobacillus, Lentilactobacillus and Secundilactobacillus. Comparative genomics also facilitated the 3 of 3 identification of novel metabolic traits including the metabolism of phenolic compounds, formation of kokumi-active γglutamyl peptides and anaerobic respiration. Conclusions. Genome sequencing has become a routine tool for analysis of strains that are used in research or in commercial applications. In conjunction with the wealth of metabolic and physiological data that is available for lactic acid bacteria, comparative genomic analysis greatly facilitates and accelerates the selection of strains for applications in traditional or novel fermented foods.

Dr. Jennifer Ronholm, Assistant Professor – McGill University

Dr. Ronholm obtained her BSc in Microbiology from the University of Waterloo in 2007 and her Doctoral degree in Microbiology and Immunology from the University of Ottawa in 2013. She completed post-doctoral training at McGill University and at Health Canada. She was hired as an Assistant Professor in the Faculty of Agricultural and Environmental Sciences in 2017. She is a World Economic Forum Young Scientist and William Dawson Scholar. In 2020 she won her Faculty’s award for teaching excellence. Her research interests including trying to understand the role that the composition of the microbiome plays in determining susceptibility of individuals (both humans and farm animals) to bacterial infections.


The role of Genomics in Reducing the Need for Antibiotic Use in Milk Production

Bovine mastitis is a complex disease that is usually caused by a bacterial infection involving one of many possible pathogens. Mastitis infections cost the Canadian dairy industry about $665 million annually and result in the use of large volumes of antibiotics. However, increasing prevalence of antimicrobial resistant human infections have led to the use of antibiotics in agriculture being viewed as controversial and unsustainable. Creative use of genomic techniques may be the basis for novel prophylactics and therapeutics to reduce the need for antibiotic use in dairy farming. To investigate if the composition of the microbiome plays a role in mastitis susceptibility in dairy cattle, we collected milk samples from 698 dairy cows in Quebec once every two weeks for over a year. We used 16S rRNA targeted amplicon sequencing (TAS), whole genome sequencing (WGS), and metagenomic sequencing (MS) to compare the microbiome between cows that did and did not develop mastitis during our study period. We found that the presence of Non-Aureus Staphylococci (NAS) and Aerococcus urinaeequi in the microbiome had a protective effect against Staphylococcus aureus mastitis, and the presence of Escherichia spp., Glutamicibacter spp., Acinetobacter spp., NAS, and Aerococcus spp. each had a protective effect against both Escherichia coli and Klebsiella pneumoniae mastitis. These discoveries are being further investigated to elucidate the mechanism and develop possible probiotic strategies to negate the use of antibiotics in dairy farming.