Author Affiliations: Departments of Medicine and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California; and Veterans Affairs Palo Alto Health Care System, Palo Alto, California.
Revolutionary advances in DNA sequencing technology are radically changing the approach for studying and characterizing the microbial world. The sequencing of a microbial genome, which can now be achieved in preliminary form in hours, provides a wealth of information about the functional potential of the organism, its evolutionary relationships with other organisms, and clues about niche adaptation, and without the need for microbial cultivation or isolation.1 Likewise, so-called shotgun or metagenomic sequencing, which is the high-throughput simultaneous sequencing of random fragments from complex mixes of different genomes, provides insights into the potential activities of a microbial community, possible interactions between microbial community members, and the nature of their relationships with their environment (eg, a human host).
Relman DA. Metagenomics, Infectious Disease Diagnostics, and Outbreak Investigations: Sequence First, Ask Questions Later? JAMA. 2013;309(14):1531–1532. doi:10.1001/jama.2013.3678
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