Review on the NGS-based studies of microbiotas of artisanal and regional kinds of cheese with potential as functional foods: composition and functional analysis

This review aims to reveal and summarize the advantages and disadvantages of culture-dependent and culture-independent methods for identifying and characterizing the microbiota of artisanal regional varieties of cheese and the health benefits of these kinds of cheese as a functional food. With the rise of metagenomics studies, the focus is now on using these techniques to explore the genetic diversity in different types of cheese, identifying both known and novel microorganisms. Based on literature data, in addition to the possible roles of microorganisms included in artisanal dairy products on cheese ripening, the health-promoting effects of these bacteria are highlighted as well. The analysis of the literature data available so far showed that metagenomic analysis would allow for obtaining more accurate and rapid results. In addition, cheese microbiota and microbial interactions play an essential role in acidification and flavour development in cheese. The production of microbial bioactive compounds, their role in inhibiting pathogens and spoilage agents, and the probiotic potential are also discussed.