Next Generation Sequencing: problems and opportunities for next generation studies of microbial communities in food and food industry

Food sciences has tried from the very beginning to describe the species present in various substrates, foods and beverages and to describe the changes of the microbiota during food evolution and maturation. These investigations require tools to massively identify bacteria and fungi in a taxonomically sound way. Next Generation Sequencing is a very promising tool in this perspective for its unmatched ability to detect sequences of taxonomic and functionally important genes. This paper reviews the variants of NGS technology and their possibility of application in various fields of food sciences, with remarks on drawbacks and possible solutions implying modifications of the molecular procedures or the application of advanced bioinformatics to interpret, store and re-use the data coming from the NGS-based studies in food microbiology.