Methods to Study Metagenomics

Metagenomic profiling of human fecal samples has long uncovered the importance of the microbiota in human health and disease. In recent years, metagenomic studies have demonstrated that the microbes that inhabit the human body have important commensal roles far beyond aiding digestion in the intestinal tract, leading the human microbiome to be defined as an endocrine organ in itself. In order to study these microbial communities, researchers have had to develop different methodologies to accurately characterize them, and to identify which microbes are commensal, and which can be considered pathogenic. In this chapter, we will discuss the next-generation sequencing methods of metagenomic profiling, which have made the expansion of our knowledge possible. Starting from more targeted approaches to untargeted ones, we will discuss the pros, cons, and potential applications of each sequencing strategy. Finally, we will introduce the recent advancements in third-generation sequencing technology, discussing the implications of the emergence of this new approach for the field of metagenomics.