Another day, another genome…or 56…
Just caught the announcement via GenomeWeb that the GEBA project paper has been published with 53 bacterial genomes (see Nature for a summary article that is available, and the paper itself is here). They deliver 53 bacteria and 3 archaea.
GEBA is the Genomic Encyclopedia of Bacteria and Archaea. They developed a strategy to select microbial genomes not because of some important physiology of that microbe, or because it was a disease-causing organism, but more based on looking across the world of species via phylogeny, and selecting some that might have been otherwise neglected. This is a neat strategy in many ways, because usually we only look under the flashlight for stuff we are kinda looking for already. This turns that around and looks in the dark as well. That does make it something of a fishing expedition, and I can understand those criticisms of an approach like that. But we are sure to learn useful things from stuff we weren’t really looking for too.
Have a look at the paper and consider that strategy.
A great place to look at the organisms online will be IMG, the Integrated Microbial Genomes database. They have a special subset of IMG/GEBA available here: http://img.jgi.doe.gov/cgi-bin/geba/main.cgi . We’ve got a tutorial on using IMG that covers the main aspects of the IMG foundation as well (requires subscription).
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B., Hooper, S., Pati, A., Lykidis, A., Spring, S., Anderson, I., D’haeseleer, P., Zemla, A., Singer, M., Lapidus, A., Nolan, M., Copeland, A., Han, C., Chen, F., Cheng, J., Lucas, S., Kerfeld, C., Lang, E., Gronow, S., Chain, P., Bruce, D., Rubin, E., Kyrpides, N., Klenk, H., & Eisen, J. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Nature, 462 (7276), 1056-1060 DOI: 10.1038/nature08656
UPDATE: Jonathan Eisen, one of the authors on this paper, has an excellent post up with more backstory on this work. Check it out at his blog: http://phylogenomics.blogspot.com/2009/12/story-behind-nature-paper-on-phylogeny.html
UPDATE 2: There’s a great article in the NYT on this work as well: Scientists Start a Genomic Catalog of Earth’s Abundant Microbes