Application of Next-Generation Sequencing Techniques in Food-Related Microbiome Studies

Developing next-generation sequencing (NGS) techniques has helped scientists to learn and understand the microbial ecosystem from deeper and richer insights. Contemporaneous advancements in DNA sequencing technologies have allowed not only a clearer classification of microbial communities, but also a broader phylogenetic description of complicated microbiomes which, in their molecular nature, are the collective genetic material of the microbes known to inhabit an area, whether the area is a specific body econiche (e.g., human gastrointestinal tract) or an atmosphere. To date, decoding 16S rDNA, metagenomics, and metatranscriptomics are the three fundamental sequencing techniques used to classify and characterize food-related microbiomes. These sequencing techniques used various NGS frameworks for recognition of the DNA and RNA sequences. 16S rDNA sequencing has historically played a crucial role in defining the phylogenetic makeup of a microbiota associated with food. Metagenomic methods have progressively culminated in a greater knowledge of a microbiome by offering a classification at the species level/strain level. In addition, metatranscriptomic strategies have led to the computational characterization of the diverse interactions within a single microbiome between various microbial communities. Numerous reports have demonstrated the use of NGS techniques to examine fermented food microbiomes. However, the use of NGS techniques in the study of non-fermented food microbiomes is limited. This analysis offers a brief summary of the developments in DNA sequencing metabolic pathways as the technologies evolved from first, second, and third generations and illustrates how NGS offered a complete understanding of food-related microbiomes with a specific emphasis on non-fermented foods.