Metagenomics constitutes the sequence based analysis of the collective microbial genomes (microbiome) in a particular environment. It provides culture independent access to the gene pool of whole microbial community. The variety of laboratory culturing methods when fail to culture the unculturable bacteria, tools of metagenomics are applied to reveal their existence in a given environment. Metagenomics tools deal mainly with the direct isolation of genetic material from a defined ecological habitat (soil or marine) and cloning of the complete genome of the entire microbial population.