A term we heard a bunch at the Emory Microbiome Symposium in November was â€œmetagenomicsâ€. Time for an explainer, with some help from Emory geneticist Tim Read.
Nature Reviews Microbiology defines metagenomics as â€œgenomic analysis of microbial DNA that is extracted directly from communities in environmental samples.â€
This technology â€” genomics on a huge scale â€” enables a survey of the different microorganisms present in a specific environment, such as water or soil, to be carried out. Metagenomics is also emerging as a tool for clinical diagnosis of infectious diseases.
Read notes that the term specifically refers to â€œshotgunâ€ sequencing of environmental DNA.
â€œThe shotgun approach is to randomly sample small pieces of the DNA in the tube, no matter which organism they came from,â€ he says. â€œThe output is a mÃ©lange of different genes from bacteria, viruses, fungi, plants and humans.Â The data is fascinating but the analysis is daunting.â€
A related, but less comprehensive/open-ended approach (sometimes incorrectly placed under the banner of metagenomics, Read says) is microbiome census sequencing.Â Here , scientists look at the genetic variation in just one gene to count the number of different species present. Usually, to take a census of bacteria in the microbiome, the gene encoding the largest RNA subunit of the ribosome is used.
However, there are situations, for instance when scientists study the microbes that live in our intestines or on our skin, when a single gene doesn’t give enough information and shotgun metagenomics data is needed to increase the resolution of the analysis.
An example: when studying the â€œmigrationâ€ of pathogenic S. aureus bacteria within urban environments. Read and colleagues recently posted this analysis of S. aureus genomes on the preprint server bioRxiv. His team has established the website Staphopia as a resource for the community of researchers analyzing this type of data. In connection with this area of research, they re-analyzed an initially alarming report of anthrax DNA in the New York City subway.
Metagenomics is also a major tool for environmental microbiologists, who use it to study organisms that can not be cultured in isolation. With justification, some researchers have argued that this approach could be a source for biotechnology prospecting.
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