Zooming into food-associated microbial consortia: a ‘cultural’ evolution

•The evolution of the overall approach to study food microbes is reviewed.•The recent results obtained by sequencing-based approaches are examined.•The use of meta-omics techniques to address food safety issues is discussed.

Foods are complex and dynamic microbial consortia where bacteria, yeasts and fungi can coexist. The advances in the culture-independent analysis of food microbiota have revolutionized the way we study these microbial ecosystems, leading to a ‘cultural’ evolution. This is not only because we have technically learned to avoid cultivation to study food microbes, but also because our mental approach to food microbiology has changed. We discuss the most recent achievements in the field of food microbial ecology and give examples of how current molecular biology tools can be used to study performance of microorganisms used for food fermentation, to explore the sources of technologically relevant and spoilage bacteria as well as to acquire knowledge on the behaviour of foodborne pathogens.