Metagenomics is a novel method to study the collective genome of microorganisms from an environmental sample to provide information on the microbial diversity and ecology of a specific environment. Shotgun metagenomics refers to the approach of shearing DNA extracted from the environmental sample and sequencing the small fragments. Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and in human and animals health condition.
High-throughput sequencing approaches enable genomic analyses ideally of all microbes in a sample, not just those that are amenable to cultivation related to any microbial environment ranging from human gut to oceans. One such method, shotgun metagenomics, is the untargeted ('shotgun') sequencing of all ('meta-') microbial genomes 'genomics' present in a sample. Shotgun sequencing can be used to profile taxonomic composition and functional potential of microbial communities and to recover whole genome sequences.
By offering direct access to the entire genetic content of microbial communities, metagenomics can provide valuable molecular insights into novel enzymes, anti-microbial peptides, and biocatalysts, as well as into genomic linkages between community function and structure. The metagenomic approach serves as a powerful tool for elucidating the relationship between host-associated microbial communities and host phenotype.