The Use of Metagenomics in Quantitative Microbiological Risk Assessment (QMRA)

The application of next generation sequencing techniques in food samples offers the potential to investigate the microbial composition and functions in unprecedented depth and in high throughput fashion. Metagenetics, or amplicon sequencing, is an approach that is ‘taxonomy oriented’, gives a detailed view of the composition of a system and has been applied to describe the microbial ecology of foods and food-related ecosystems. Metagenomics is a ‘function’ oriented approach and has, as of yet, been less exploited in food microbiology. Both approaches can enrich our understanding regarding interactions between biotic and abiotic factors but also within the microbial community of any given ecosystem. Understanding such interactions and the behavior of microorganisms is important in the process of assessing biological risks in foods. For example, associations between specific microbial communities and the presence of a foodborne pathogen can be unraveled by the culture-independent analysis of large sets of samples. Further, such association may lead to the identification of community fingerprints to trace foodborne pathogens at species or even strain level and their transmission through the food chain. It is envisioned that risk assessment will gradually integrate information that concern the behavior of microorganisms, assembled from ‘omics’ data, and shift from the taxonomic definition of the biological hazards. Improvement of the resolution of the metagenomics data would allow us to observe and study the foodborne pathogens in their environment even when they are not prevailing components of the microbial community.