Microorganisms exist along the food chain and impact the quality and safety of foods in both positive and negative ways. Identifying and understanding the behaviour of these microbial communities enable the implementation of preventative or corrective measures in public health and food industry settings. Traditional culture-dependent microbial analyses are time-consuming and target only specific subsets of microbes. However, the greater use of culture-independent metagenomic approaches has the potential to facilitate a thorough characterization of the microbial communities along the food chain. Indeed, these methods have shown potential in contributing to outbreak investigation, ensuring food authenticity, assessing the spread of antimicrobial resistance, tracking microbial dynamics during fermentation and processing, and uncovering the factors along the food chain that impact food quality and safety. During the seminar, I will provide an overview of our research in these areas, while providing specific examples relating to specific foods and relevant food chain-related environments.