Metagenomics: a powerful lens viewing the microbial world

Abstract Metagenomics—as the name suggests—deals with the metadata of several genomes in order to provide quick and reliable information on the composition and distribution of an interacting microbial population in an ecosystem. Activities of microbial communities are an integral part of an ecosystem’s functioning. They also influence the system’s productivity and long-term sustainability. Despite several scientific and technological advancements in biology and the development of several bioinformatics tools and techniques, it is almost impossible to isolate and identify all microorganisms from any environment and culture/cultivate them separately in laboratories. The limitations of doing so restricts the comprehensive understanding and knowledge of microbial niches and the ability to mine information that was unavailable earlier. It hinders the utilization of unculturable microbial population for human purposes, for example, discovery of enzymes of industrial importance. Methods for the identification of microorganisms comprise polymeric chain reaction (PCR)-based DNA fingerprinting techniques, non-PCR-based methods, FISH techniques, and polyphasic approaches, and metagenomics. Each method has its own benefits and challenges. PCR-dependent methods need successful DNA extraction followed by efficient PCR amplification of extracted DNA for satisfactory results. Fluorescence in situ hybridization is only applicable to ribosomal RNA and gives unreliable results for cells with low ribosomal content. Metagenomics is a rapid, easy, and reliable technique performed on the sample directly obtained from the environment. It involves total genomic DNA extraction, cloning, sequencing of thus obtained DNA sequences and then screening for specific genetic markers. It circumvents the limitation of culturing microorganisms separately in laboratories. Metagenomics has a wide range of proven applications from environmental to clinical samples. It has been used for the identification of biodegradation genes and pathways for a diverse range of pollutants including organic and inorganic materials, heavy metals, pesticides, antibiotics, etc. The combination of metagenomics, metatranscriptomics, and metaproteomics approaches can further enhance the identification of novel genes, their expression level and activities in an ecosystem. Here in this chapter, we have discussed the historical development and progression in the field of metagenomics, the tools and techniques used for sequencing, and the application of metagenomics to solve the problems of humanity. Further, it elaborates challenges needed to be overcome in the field of metagenomics analysis.