A full view of foodborne microbes

Dr Matthew Gilmour discusses the new opportunities for monitoring and responding to the microbiota of foods using metagenomic sequencing.

There is a complex ecology of microbes that can exist on foods, and an even more complex ecology within the settings where foods are produced. From a food safety perspective, the longstanding view of these microbial populations has focused on priority foodborne pathogens such as Listeria and Salmonella that have established risks to human health. However, if present, these microbes are only a minor component of the total microbiota of foods and food production settings, which also include a multitude of bacterial species, such as Pseudomonas, that can dominate within natural environments.

Decades of food safety research to support regulatory and surveillance testing has provided extensive microbiology culture and molecular testing approaches that cut through the complexity of microbial communities to provide accurate and rapid measurements of individual foodborne pathogens. These tests are highly effective at detecting key pathogens by using strategies to enrich or amplify targeted microbial species that may exist at very low levels in samples collected from foods or food production settings.

Another tactic to address the complexity of food microbiota is to perform metagenomics – genetic sequencing of the entire or an enriched population of microbes, which reveals the microbiome. In an increasingly cost‑effective manner, genome sequencing platforms can acquire vast amounts of genetic data that are sufficient to reveal the full microbiome in samples collected from the food chain, while still providing a depth of valuable information on individual key pathogens. Metagenomic sequencing of food‑chain samples is now under active research and development by multiple research groups with collaboration with food producers.