Tag Archives: geba

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).

You might also consider “adopting a genome” from the GEBA project as some schools have done!  Trey talked about that one week as a Tip-of-the-Week .

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

Tip of the Week: Genomic Encyclopedia of Bacteria & Archaea (GEBA)

Being summer, a strangely slow connection and some other factors, I am embedding a talk from Doug Ramsey (posted on SciVee) on the GEBA project at JGI (instead of doing a tip myself :). The GEBA project recognizes that many, if not most, of the bacterial and archaeal genomes that have been sequenced to date have some relevance to human disease or other human interest. This of course is reasonable, but it also leads to big gaps in our knowledge of bacterial evolution and genomics, knowledge that would help us better understand those genomes that we find relevant and knowledge that in and of itself can be quite interesting and potentially useful. View the talk to learn more about this project to sequence 100 phylogenetically diverse bacterial and Archaeal genomes.
I’m also posting this as an introduction to JGI’s Adopt a Genome project. This project allows student groups to adopt and study a bacteria in the GEBA project and hopefully add to our knowledge and annotations of the genome while learning. The students can then annotate the adopted genome by using IMG-ACT.