Current perspectives in food-based studies exploiting multi-omics approaches

•Bioinformatics tools have been developed to provide information on microbe diversity.•Shotgun metagenomics is a promising approach to discover the functions of microbiota.•Data generated through a multi-omics approach can improve the knowledge on what happens in food.

The new frontiers of microbial ecology are concerned pertain to what microbes are do in a complex ecosystem, such as food, and how the environmental conditions (e.g., changes in the process parameters, storage temperature, the addition of a starter culture and changes in ingredients) can affect the development and functioning of microbiota. A multi-omics approach can help researchers to obtain an unprecedented insight into the mechanisms that can affect the final characteristics of products, in term of organoleptic proprieties, as well as safety.