UPDATE: Our paper on this topic is out and there has been a bit of news here and there about it (e.g., NyTimes). For more see
- More coverage of the GEBA “Phylogeny Driven Genomic Encyclopedia”
- Story Behind the Nature Paper on ‘A phylogeny driven genomic encyclopedia of bacteria & archaea’ #genomics #evolution
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Nice little story in Nature News about the need to sequence “neglected” microbes.
Biologists rally to sequence ‘neglected’ microbes : Nature News
Quotes me and a few others. Love the fact that it quotes Steven Giovannoni in support of this notion:
“The broad brush strokes of microbial diversity are not adequately represented in that first thousand,” says Stephen Giovannoni, a microbiologist at Oregon State University in Corvallis. “It’s absolutely important that we sequence more.”
I like this because Steve gave me enormous grief about this project at a conference last year. Though I argued with him and disagreed with him, his critiques helped guide much of our work on this project that helped make our paper on the work (which is in press) much better. Glad he generally is now in support of this type of project, though not sure what he thinks about our work in this area …
Here are some of my quotes:
“There’s no doubt to us that filling in the branches of the tree is going to be useful to lots of scientific studies that use genomic data,” says Eisen. “There have been four billion years of evolution and we can really benefit from having some of that information in our databases.”
All these new genomes should improve researchers’ understanding of the evolution, physiology and metabolic capacity of microbes, says Eisen. They will also help match DNA sequences to their proper species from large-scale, high-throughput metagenomic studies from environmental samples, and ultimately contribute in the fields of synthetic biology and genetic engineering.
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Jonathan Eisen's Lab 
Jonathan — do you know if anyone is “coordinating” these various microbial efforts? Here at UW-Madison a group led by Nicole Perna is tooling up to sequence 100 members of the Enterobacteriaceae under NSF's “Assembling the Tree of Life” funding. Here's a link to the award abstract. We don't have a web site up yet, but have picked our first 25 genomes …
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Nobody coordinates anything – best place to find information is Genomes Online .
I note that, however cool and important I think your project is, Enterobacteriaceae are not exactly “neglected” 😉
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The Enterobacteriaceae are not “neglected,” but the current coverage is decidedly skewed towards Escherichia/Shigella, Salmonella, and Yersinia … and yes, I'm fully aware that I contributed to said skew.
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isnt it nice how phylogeny is kind of fractal? zoom in on one family and you can still say some parts are well covered and others are not …
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