Environmental Shotgun Sequencing (ESS). (A) Sampling from habitat; (B) filtering particles, typically by size; (C) DNA extraction and lysis; (D) cloning and library; (E) sequence the clones; (F) sequence assembly. doi:10.1371/journal.pcbi.1000667.g001

A metagenome is a collection of the entire genomes of multiple different microorganisms from a particular source. A sample is taken directly from any type of environment ranging from a mountain top lake to the hind gut of a reindeer. The DNA is then collectively extracted and analyzed.This allows scientists to study genetic characteristcs of numerous species of microbes without the need to isolate pure colonies in a laboratory setting.

Metagenomics, also called ecogenomics, environmental genomics and community genomics, is the study of these metagenomes. This emerging field grants access to the genetic information of countless microbes that do not culture easily, or at all. Metagenomics therefore opens up new possibilities for applications in human health, biotechnology, and numerous environmental studies.

Wikipedia: Metagenomics

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