The terms intestinal "microflora" or "microbiota" refer to the microbial ecosystem colonizing the gastrointestinal tract. Recently developed molecular biology instruments suggest that a substantial part of bacterial communities within the human gut still have to be described. Intestinal bacteria play an essential role in the development and homeostasis of the immune system. Most of these important microbiota are unculturable which significantly have limited our understanding of bacterial-host crosstalk. Among the methods designed to gain access to the physiology and genetics of uncultured organisms, metagenomics, the genomic analysis of a population of microorganisms, has emerged as a powerful technology. Metagenomics is the study of genomic content in a complex mixture of microorganisms. Direct isolation of genomic DNA from an environment circumvents culturing the organisms under study. The two primary goals of this approach are to develop a consensus of what populations of microorganisms are present and then to identify what roles each microorganism has within a specific environment. Metagenomics samples are found nearly everywhere, including several microenvironments within the human gut, soil samples, extreme environments such as deep mines and the various layers within the ocean. Therefore, the diversity of microorganisms is thought to be in the range of hundreds of millions to greater than tens of trillions of species. Among the most mysterious microenvironment is the human gastrointestinal tract that harbor greater than thousands of millions of microbial species (at least 1014), including up to 2000 species dominated by anaerobic bacteria.