A primary motivation for metagenomics is that most microbes found in nature exist in complex, interdependent communities and cannot readily be grown in isolation in the laboratory. One can, however, isolate DNA or RNA from the community as a whole, and studies of such communities have revealed a diversity of microbes far beyond those found in culture collections.
The Metagenome Program Products include Metagenome standard draft; Metagenome minimal draft; Metatranscriptome and 16S tag sequencing. By scaling current methods we can now describe the functional content of a microbial community in the form of a “catalog of genes.” Larger-scale experiments involve analysis of the response of microbial communities to natural environmental variation and experimental perturbation; the dependence of symbiotic microbial communities on the genotype and phenotypic state of their hosts; and the sampling of metagenomes across hundreds of diverse environmental conditions.
The Metagenome Program major strategic efforts include:
Terrestrial Carbon Cycling: These include the Great Prairie Grand Challenge Project; the San Francisco Bay/Delta Wetlands Project; Rangelands; and Soil and Peatlands Community Science Program (CSP) Projects.
Plant-Microbe Interactions: These include the studies of the rhizosphere and endosphere of Arabidopsis, Poplar and Maize, and a project focused on root-enhanced decomposition.
Technology Development & Data Analysis: Several projects target improved metagenome assembly and genome binning, data interpretation via metagenome visualization, identification of protein and operational taxonomic unit (OTU) clusters, and generation of full-length 16S sequences on the PacBio platform.