Metagenomics, also known as shotgun metagenomics sequencing, is the comprehensive study of the nucleotide sequences from all microorganisms in a sample. It is used to study specific communities of microorganisms and overcomes challenges of unculturable and diverse microbes. It focuses on microbial diversity, genetic relationships, functional activities, and interactions with the environment. Clinical applications for metagenomics include diagnosis of infectious diseases, outbreak tracking, and mutation and pathogen discovery.