Next generation microbiological risk assessment meta-omics: The next need for integration

The development of a multi-omics approach has provided a new approach to the investigation of microbial communities allowing an integration of data, which can be used to better understand the behaviour of and interactions between community members. Metagenomics, metatranscriptomics, metaproteomics and metabolomics have the potential of producing a large amount of data in a very short time, however an important challenge is how to exploit and interpret these data to assist risk managers in food safety and quality decisions. This can be achieved by integrating multi-omics data in microbiological risk assessment. In this paper we identify limitations and challenges of the multi-omics approach, underlining promising potentials, but also identifying gaps, which should be addressed for its full exploitation. A view on how this new way of investigation will impact the traditional microbiology schemes in the food industry is also presented. •Omics represent valuable tools to produce behavioural and interactions data in microbial communities.•NGS produces data about ecology (metataxonomics), gene presence (metagenomics) and its transcription (metatranscriptomics).•Metagenomic libraries can allow the reconstruction of pathogens genome then used for Genome Scale Metabolic Models (GSMM).•Integrating omics data into MRA will have an impact in food safety, but also to better control spoilage processes.