Microbes are present almost everywhere. They play a vital role in cycling carbon, release important compounds, and may be associated with infectious diseases. Metagenomics is the culture-independent genomic research of microbial communities. Metagenomics presents a powerful tool to study prokaryotes and viruses in the environment via the analysis of their DNA obtained directly from environmental samples. This technology considers the DNA of microbes in a population as a whole. It can not only identify the microbial of microbial species present but also provide insight into the functional roles and metabolic activities of the microorganisms. The coupling of this method with function-based activity is a powerful technique for the discovery of new functional genes from uncultured microbes.