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Metagenomic approaches are a growing branch of science and have many applications in different fields. Metagenomics seems to be the ideal cultureindependent technique for unraveling the biodiversity of soils and to study how this biodiversity is affected with continuously changing conditions. In addition, its application in clinical and diagnostic approaches was reported. The emergence of several next-generation sequencing (NGS) strategies enriched the metagenomics. The combination between NGS and metagenomic approaches helped the investigators resolve several issues regarding the microbial diversity and the functions and relationships among different microbial flora. A number of NGS approaches were developed including Roche/454 pyrosequencing, Illumina/Solexa sequencing, and Applied Biosystems/SOLiD sequencing. In this chapter, different NGS platforms are discussed in terms of principle, advantages, and limitations. In addition, thirdgeneration sequencing technologies are also addressed.

Screening for microbial secondary metabolites (SMs) has attracted the attention of the scientific community since 1940s. In fact, since the discovery of penicillin, intensive researches have been conducted worldwide in order to detect and identify novel microbial secondary metabolites. As a result, the discovery of novel SMs has been decreased significantly by using traditional experiments. Therefore, searching for new techniques to discover novel SMs was one of the most priority objectives. However, the development and advances of omics-based techniques such as metabolomics and genomics have revealed the potential of discovering novel SMs which were coded in the microorganisms' DNA but not expressed in the lab media or might be produced in undetectable amount by detecting the biosynthesis gene clusters (BGCs) that are associated with the biosynthesis of secondary metabolites. Nowadays, the development and integration of gene editing tools such as CRISPR-Cas9 in metabolomics provide a successful platform for the identification and detection of known and novel SMs and also to increase the production of SMs.

Metagenomic is a promising technique that has many applications in different fields. In fact, metagenomics is the ideal culture-independent technique that unravels the microbial composition and biodiversity in the sample, which helps scientists to study and understand how this biodiversity is affected by continuously changing conditions in the environment and how this microbial community interacts with each other. In the past, the microbial composition in extreme environments was undiscovered due to the difficulty of isolation, culturing, and identification of microbes living there. However, nowadays after the development and combination of metagenomic and next-generation sequencing techniques, it became more easy to study the microbial composition in extreme environments without culturing. In this chapter, the use of metagenomic techniques to study the microbial biodiversity in different extreme environments are discussed. In addition, different NGS platforms are discussed in terms of principles, advantages, and limitations.