Sequencing technologies have deeply changed our approach to the study of food microbial communities. This review describes recent exploitations of high-throughput sequencing applications to improve our knowledge of food microbial consortia. In the past 10 years, target amplicon sequencing has become routinely used in many food microbiology laboratories, providing a detailed picture of food-associated microbiota. Metagenomics and metatranscriptomics approaches are still underexploited in food microbial ecology, despite their potential to uncover the functionality of complex communities. In a near future, sequencing technologies will surely advance our understanding of how to effectively use the invaluable microbial resources to improve food quality and safety.


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