Metagenomics Approaches for Improving Food Safety

Abstract

Advancements in next-generation sequencing technology have dramatically reduced the cost and increased the ease of microbial whole-genome sequencing. This is revolutionizing the identification and analysis of foodborne microbial pathogens, facilitating expedited detection and mitigation of foodborne outbreaks, improving public health outcomes, and limiting costly recalls. However, this approach is still anchored in traditional laboratory practice involving the selection and culture of a single isolate. Metagenomic-based approaches, including metabarcoding, shotgun and long-read metagenomics, comprise the next disruptive revolution in food safety diagnostics and offer the potential to directly identify entire microbial communities in a single food, ingredient, or environmental sample. In this review, metagenomic-based approaches are introduced and placed within the context of conventional detection and diagnostic techniques, and essential considerations for undertaking metagenomic assays and data analysis are described. Recent applications of the use of metagenomics for food safety are discussed, alongside current limitations and knowledge gaps, and new opportunities arising from the use of this technology.