Metagenomics studies genetic material collected from a mixed community, often without first culturing its members separately. DNA sequencing can reveal community composition and potential metabolic capacities. A detected gene indicates sequence potential; its expression and actual contribution to metabolism require additional evidence. Genome assembly from mixed samples is difficult because closely related organisms can share sequences and differ in abundance. [ref]
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Metagenomics is the study of genetic material recovered directly from environmental samples, allowing researchers to analyze the collective microbial genomes present in a particular habitat without the need for isolating and culturing individual species. This field of research leverages advanced sequencing technologies to explore the diversity, functional potential, and interactions of microorganisms in complex communities.
Experiments that involve sequencing bulk DNA found in a sample to determine what species are present, as opposed to sequencing just a single specific specimen. Examples of samples that are often used:
- river water to determine which bacteria are present, notably to determine if the water is free of dangerous bacteria. A concrete example is shown at: Section "How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it".
- sea water biodiversity: ocean-microbiome.embl.de/companion.html
- food, including searching for desirable microorganisms such as in cheese or bread yeast
- poo, e.g. to study how the human microbiome influences health. There are companies actively working on this, e.g.: www.microbiotica.com/
One related application which most people would not consider metagenomics, is that of finding circulating tumor DNA in blood to detect tumors.