Metagenomics is the culture-independent analysis of a mixture of microbial genomes using an approach based either on expression or on sequencing. The term is derived and coined from the statistical concept of meta-analysis and genomics to capture the notion of analysis of a collection of similar but not identical items. The meta-analysis is a process of statistically combining separate analyses, that is, analysis of analysis. Metagenomics is the application of the methods of genomics to microbial assemblages. It involves studying the genetic makeup of many microbes in an environment simultaneously, and makes accessible the many types of microbes that cannot be grown in the lab and therefore cannot be studies using the central tool of classical microbiology. Metagenomics also enables the study of entire microbial communities, offering a window to intact microbial system. The emerging field of metagenomics presents the greatest opportunity to revolutionize understanding of the living world.