Sunday, October 25, 2009

A field guide to the microbes?

Here is a link to an article in Microbe Magazine (Genomic Analyses Could Lead to “Field Guide to Microbes”) discussing in part a session from last years ASM Meeting on the "1$ Bacterial Genome". The article includes a discussion of my proposal to create a "Field Guide to the Microbes." Also the article has a link to an audio interview of me by the article author Jeffrey Fox.

Audio interview with Jonathan Eisen

The article does not quite capture what I mean by a Field Guide to the Microbes (not the authors fault - my talk did not capture this either). But I will be writing more on this soon. Very soon. Stay tuned. Also here are the slides from that talk, which I posted to slideshare

Also see this talk I gave at the JGI User Meeting where I ended with my call for a Field Guide to the Microbes ...


  1. You do realize that there is such a book in existence -- Betsey Dyer's Field Guide to Bacteria. Not saying that it couldn't be improved; just that people ought to read it first.

  2. I like that book - but it is not really a field guide. It is more of a catalog of fun examples.

  3. Brandon Iker10/25/2009 6:57 PM

    Dr. Eisen,

    Thank you for the great talk in philly! Your post, and the current genome that my group is attempting to sequence, popped an idea in my head about a potential technique that could be used in the quest for less expensive sequencing and analysis. Have you had any thought on using competitive genome hybridization or genome fragment enrichment(GFE) techniques when attempting genome sequencing of closely related organisms?

    By using GFE, sequencing efforts could be more focused and efficient by only focusing on genome regions that show dissimilarities, e.i. this would make things less computationally intensive and less expensive. GFE may allow us to fill in some gaps in our more "well studied" phylogenies, and at the same time free up money, time, and effort for more rare genomes.

    Not that I am necessarily proposing anything but just some food for thought and the result of a funky idea.

  4. For big genomes that would make sense Brandon and I think I have heard of people doing it. But for microbes, especially bacteria/archaea, it is probably not worth it. Right now with a mix of 454 and Solexa (or, if you go by company names, Roche and Illumina) one can sequence to near completion a bacterial genome for < $1000. Soon that will certainly be < $100. Does not seem worth it to add any complexities to the DNA prep phase ...


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