One application of DNA sequencing is the field of metagenomics, the culture-independent study of genetic material recovered directly from environmental samples. Metagenomics describes the functional and sequence analysis of the collective microbial genomes contained in an environmental sample. The term is derived from ‘meta’ (in this case meaning an overarching understanding of genetic diversity) and ‘genomics’ (the comprehensive analysis of an organism's genetic material).
While not a new discipline, metagenomic applications have experienced a huge boost due to the new possibilities that exist with next-generation sequencing technologies.
Estimations suggest that only 1% of all microorganisms are cultivable, therefore metagenomic research may dramatically broaden our knowledge of environments.
For many years, the term “metagenomics” was only connected with the analysis of environmental samples, for example the analysis of DNA isolated from extreme habitats to identify new biocatalysts for industrial applications. However the dramatic increase in throughput, together with the decreases in cost and time has considerably broadened this field to new applications.
Metagenomics can be divided into several areas, including:
Note: This is not an exhaustive list and researchers may choose other criteria.
Pathogenomics/infection genomics is related to diagnostics and is the identification of unknown pathogens from a symptomatic patient. This is often a challenging process since the number of microbes may be very low (~1–10 cells/ml blood).
Conversely, in microbiome analysis, there is a high amount of microorganisms, e.g., from oral or fecal swabs. Here, the aim is to analyze the composition of the community. Given that a human body consists of only 1% human cells and 99% microbial cells, microbiome analysis has a significant potential for future diagnostic applications. See the “Human Microbiome Project (www.hmpdacc.org) for more detail.
In environmental metagenomics, the focus — in addition to the classical search for new biocatalysts — is the investigation and characterization of habitats.
Principally, there are two different approaches:
Whole genome analysis: every DNA present is sequenced
16S profiling: only 16S rRNA DNA is sequenced
The first approach is simply sequencing every DNA present in the sample. This gives the most complete picture of the microorganisms present and may, for example, identify new enzymes/enzyme classes, as well as antibiotic resistances. On the other hand, it requires higher sequencing capacities resulting in lower throughput and higher costs than the second approach. Further methods are in development.
In metagenomic applications, typically sequencing instruments giving higher read-lengths are necessary because there is usually no reference sequence available. Also for 16S rRNA profiling, a sequencing system is required whose read-length spans the whole region (see also NGS sequencers).