ABSTRACT
The availability of genomic information in recent years has been explored rapidly due to the impact of next-generation sequencing (NGS) techniques, leading to an increased number of sequenced genomes from a broad spectrum of organism. At a time, thousands or millions of sequences can be produced by using high-throughput technology like NGS. Additionally, the limitations implied by the short-read sequencing platforms, where the sequenced genomes lack these techniques, have overcome entire genomic content. This sequencing technology allows identifying microbial taxa from unculturable or even from organisms present in small numbers more accurately. Further, NGS technology also identifies all microbial genes and operons or differential expressed genes at various conditions. The introduction of NGS strategies has revolutionized microbial ecology, which allowed us to investigate several food ecosystems. This chapter discusses standard NGS techniques and platforms focusing on the study of food microbiota. Furthermore, several in silico approaches implemented to optimize the genome assemblies that facilitate on finishing process of genome sequencing and the contribution of NGS to a systems-level understanding of food microorganisms were discussed.
