Nothing like being lazy on a nice Autumn weekend. If you are so inclined, and yet you are wondering about metagenomics and specifically about what it has done for our understanding of the microbial world, here’s a satisfying piece by Hugenholtz and Tyson. For those who can't wait to read it, here are some of the main conclusions.
Among other things, microbial metagenomics:
- reveals natural communities in their richness and complexity. Metagenomics can not only identify the principal partners of a microbial consortium but also many of their metabolic capabilities.
- has great potential for stumbling across novel findings, some of which have significantly altered our view of global processes. One example is proteorhodopsin, the light-driven proton pump, discovered to be abundant in microbes in marine habitats where there is light.
- is able to reconstruct whole genomes, though currently only for prokaryotes, and it works best in simple communities with a dominant species.
- tells us about the variation in natural populations, thus providing insight into the evolutionary processes that have shaped those genomes. For example, in the most abundant photosynthesizer in oceans, Prochlorococcus, greatest variation is seen in genomic islands, likely resulting from virus-assisted lateral transfers.
- demonstrates that we have scarcely begun to discover the diversity that is out there.
But there are limitations. As sequencing costs drop, the amassing of huge numbers of sequences is outstripping computational capacity. Eukaryote genomes are still to be avoided. And if you dream of doing comparisons of every sequence against every sequence, you'll likely have to wait for a new generation of computers. Nice to know that the bottleneck is not with microbiology, but in somebody else’s bailiwick, instead.