The metagenomics is a field that directly analyzes species identification, community structure, ecological function and metabolism of microbes in their native environment.In general, 454pyrosequencing platform is most widely used in microbial metagenomics since it produces longer reads (ca.600bp) than other next generation sequencing (NGS) platforms like Illumina or Solid.Consequently, the relatively longer reads in a 454 platform keep intact information of the genes.