A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies.

Yu Cao,Shabarinath Srikumar,Kieran Jordan,Sinéad Proos,Séamus Fanning

doi:10.3389/fmicb.2017.01829

Abstract

The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents) or a food manufacturing facility econiche (e.g., floor drain). To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods.

Highlights

It is well known that foodborne diseases cause considerable morbidity and mortality in humans in immunocompromised individuals and in young children (Stein et al, 2007; Tauxe et al, 2010)
Of all the publications using different next generation sequencing (NGS) techniques in the analysis of food microbiome more than half (63%) used 16S rDNA sequencing, suggesting that this strategy was widely applied for the analysis of food/food production related studies (Figure 1B)
Using a 16S rDNA sequencing-based approach, it was shown that the microbiome of milk containing silos was influenced by that of the bulk milk tankers feeding them, and that distinct bacterial communities were evolved within different milk silos

Summary

Introduction

It is well known that foodborne diseases cause considerable morbidity and mortality in humans in immunocompromised individuals and in young children (Stein et al, 2007; Tauxe et al, 2010). Since 16S rDNA sequencing has become one of the most popular techniques to identify the microbiome members associated with food matrices. The main advantage of metagenomic approaches over 16S rDNA sequencing is the ability to characterize bacteria present in the microbiome to their species/strain level.

Results

Conclusion