Metagenomics is the study of genetic material (metagenome) recovered directly from environmental samples. In these environmental samples the genetic information of mul- tiple microorganisms is present simultaneously and, unlike traditional genomics which relies on cultivated and cloned cultures, metagenomics focuses on sequencing the DNA of the whole diversity of organisms in vivo and without in vitro cultivation. The three basic questions metagenomics aim to answer are: