The field of metagenomics arguably represents the area of study whose methods have been most affected by the development of NGS technologies. Broadly defined as the study of genetic material recovered directly from environmental samples, metagenomics makes great use of new sequencing technologies that allow for the detection of small amounts of genetic material while analyzing many different samples in parallel. The study of the microbiome, which for humans most often focuses on an analysis of material found in the gut, can be considered a subfield of metagenomics.
As DNA sequencing costs per any given metric have dropped, the number of applications that can use DNA sequencing methods have increased. One such application is the use of DNA sequencing to identify the content of any give sample, whether it’s dirt, water, or air. When the technology was expensive, only specific organisms that were well known and cultured could be reasonably analyzed. This need to culture individual microbes for analysis greatly limited the diversity of organisms available for study, but it was necessary to produce enough DNA of a single kind for input into existing sequencing technologies. Now, in the context of NGS, genetic material can be analyzed free of the need for isolation and culture. DNA extracted from environmental samples can now be sequenced directly and sequencing can be used to identify the contents of the sample. Even minor components of the original sample can be found in the NGS data provided the sequencing is “deep” enough. This opens up exciting possibilities for environmental and ecological research related to fields such as public health (e.g. water quality testing) and agriculture (e.g. soil pathogen testing).
The sequencing technique of 16S rRNA sequencing has become almost synonymous with microbiome or metagenomic research. However, it’s worth noting that many researchers take issue with the use of “metagenomics” when discussing these targeted sequencing techniques. This is because the general rRNA profiling technique only focuses on a single gene that is not representative of the whole genome. Depending on the application, 16S profiling may not provide enough resolution in terms of identifying the components of the sample being studied. When specificity is needed down to the strain level, for example, most often a WGS approach is used. Since WGS, by definition, studies the complete genome of the organism in question it is WGS and related techniques that are more properly designated as “metagenomics” in related literature.
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