ABSTRACT
For most of the environmental samples as many as 99% of the microorganisms cannot be cultured by standard culture techniques. The classic microbiological methods, which rely on phenotypic characterization of cultivated strains, are indirect and produce artificial changes in the microbial community structure. In this regard, metagenomics has merged as a powerful tool to explore unculturable microbes through the sequencing and analysis of DNA extracted from the environmental samples as well as using experimental methods, such as DNA hybridization, gene expression, proteomics, metabolomics, and enzymatic screening. The advent of metagenomicsbegan in the late 1990s, providing a new lens to discover and benefit from unculturable microbial communities. Furthermore, together with other omics approaches (i.e., genomics, single-cell genomics, metatranscriptomics, metaproteomics, and metabolomics), metagenomics provides a more multi-faceted insight into the studied biological systems compared to traditional approaches. Altogether, multi-omics approaches can provide a means to access, characterize, and quantify this untapped diversity of microbes, discovers novel genes, metabolic pathways, and essential products with biotechnological, pharmaceutical, and medical relevance. This chapter summarizes and discusses the basis of new initiatives, including metagenomics and other omics approaches that link phylogenetic and functional information about the microbiota of environments dominated by microorganisms that are refractory to cultivation.
