Impact of Next Generation Sequencing Techniques in Food Microbiology

Abstract

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 fish-derived 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.

High-Throughput Sequencing Technologies and new Approaches in Food Microbiology

“…Similar results were obtained with aromatic spices [27]. Furthermore, the integration of metabolomics technique with other technologies is important to allow the link among microbial metabolites and sensorial attributes [28].…”

Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches

“…It is characterized by a high-throughput data yield from a single run. HTS or NGS is the catch-all term used to describe a number of modern sequencing techniques including Roche/454 technology, Illumina (Solexa) technology, ABI SOLiD technology, Ion torrent: Proton/PGM sequencing and PacBio SMRT (Mayo et al, 2014). It has provided new platforms to investigate all kinds of microbial communities and to discover some rare and even unknown species.…”

“…These sequences help in identifying rarely culturable or unculturable microbes in a sample. HTS also gives an accurate inventory of all microbial operons and genes that are present or are expressed under certain study conditions (Mayo et al, 2014). Compared to DGGE, HTS can provide more detailed information with digitalized results (Ling et al, 2010).…”

PCR-DGGE for the profiling of cheese bacterial communities: strengths and weaknesses of a poorly explored combined approach

“…In the last decade, the introduction of newly developed sequencing strategies, commonly referred to as next-generation DNA sequencing techniques, has substantially revolutionised the study of genomics and molecular biology, being also successfully applied in food microbiology (Mayo et al 2014). However, the recent few studies exploiting and comparing high-throughput sequencing and PCR-DGGE surprisingly demonstrated how the latter technique still represents a valid tool for the profiling of complex food microbial communities (Delgado et al 2013;Garofalo et al 2015).…”