Metagenomics is the technique of retrieving microbial genome directly from the environmental samples regardless of the nature of sample and abundance of microbial entities. Metagenomic analysis explores the entire genetic composition of the microbial communities by sequencing and subsequent analysis. Metagenomic sequencing has been used to study the epidemiology of a variety of infectious disease agents. Metagenomics currently is used to describe microbial populations in water and sediment to understand community structure and the role of microorganisms in ecological processes. Throughout the world, it is being used in many circumstances.

In our institution, currently metagenomics have been used to see overall prevalence of bacteria, virus, and other microorganism from stool sample along with virulence factors, antimicrobial resistance genes and possibly markers of horizontal gene transfer. Previously, metagenomics was used to study gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal from scat samples.