Understanding the Maxam-Gilbert and Sanger sequencing as the first generation, in recent years there has been
an explosion of newly-developed sequencing strategies, which are usually referred to as next generation sequencing
(NGS) techniques. NGS techniques have high-throughputs and produce thousands or even millions of sequences at the
same time. These sequences allow for the accurate identification of microbial taxa, including uncultivable organisms and
those present in small numbers. In specific applications, NGS provides a complete inventory of all microbial operons and
genes present or being expressed under different study conditions. NGS techniques are revolutionizing the field of microbial
ecology and have recently been used to examine several food ecosystems. After a short introduction to the most
common NGS systems and platforms, this review addresses how NGS techniques have been employed in the study of
food microbiota and food fermentations, and discusses their limits and perspectives. The most important findings are reviewed,
including those made in the study of the microbiota of milk, fermented dairy products, and plant-, meat- and fishderived
fermented foods. The knowledge that can be gained on microbial diversity, population structure and population
dynamics via the use of these technologies could be vital in improving the monitoring and manipulation of foods and fermented
food products. They should also improve their safety.
Keywords: Next generation sequencing, NGS techniques, Pyrosequencing, Illumina, Food microbiology, Molecular microbial
ecology, Food ecology.
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