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No trip to Yellowstone?

Posted by ehamilto on 05 Feb 2009 at 16:45 GMT

I was disappointed to see that you acquired your strain from the German Collection of Microorganisms and Cell Cultures, instead of isolating it directly from Toadstool Spring, an alkaline siliceous hotspring in Yellowstone National Park.

RE: No trip to Yellowstone?

jeisen replied to ehamilto on 05 Feb 2009 at 17:50 GMT

Actually Eileen, much as we would have liked to go and collect as part of this project, we were following the recommendations of a letter published in Nature a few years ago, of which I was one of the coauthors (Ward et al. "Sequenced strains must be saved from extinction" PDF is available on my web site here . In this paper, we pointed out that there were many genomes that had been sequenced for strains that were not available. So we suggested that people (1) use type strains for sequencing if all else was equal and (2) deposit strains in culture collection. In the end, even better than depositing in culture collection is actually obtaining the strain from the collection (and therefore guaranteeing that what is sequenced is something other people can have access to). So - given that I was an author on this letter and have been a big supporter of such a protocol, it seemed unwise to do otherwise. Fortunately, with metagenomics, we all need to go out to the field to gather samples ...