Monday, January 07, 2013

Reading in detail Carl Woese's 1998 "Manifesto on Microbial Genomics" for the first time ...

I am a bit stunned by this paper from Carl Woese in 1998 which I was aware of but have not read in detail until now: - Current Biology - A manifesto for microbial genomics

I re-discovered it because I am making a compilation of papers by Woese in relation to the tribute page I have set up.  And the title (a manifesto about microbial genomics) combined with the date (1998 - early in the genome sequencing era) struck me as something worth looking at.  Plus I knew others (e.g., Phil Hugenholtz, Nikos Kyrpides, ...) had mentioned this paper to me so I figured - hey - how about actually reading it in detail.  And fortunately it is freely available at the Current Biology web site (not sure why that is actually).  Anyway - what I found in the paper is basically an argument for much of my career from 1998-2008.

Some choice lines in here but the crux is as follows
The first order of business in microbial genomics should be a phylogenetically representative genomic screen of the microbial world. In other words, all the major microbial taxa and their subdivisions — which are the major source of biological diversity on Earth — should be represented by several genome sequences. There are now more than 30 recognized major eubacterial taxa — each the phylogenetic equivalent of a eukaryotic kingdom — and at least half that number in the (far less well characterized) Archaea; not to mention the yet-to-be-discovered kingdoms among the unicellular eukaryotes.
This basically lays out the Tree of Life project I co-ran at TIGR and the Genomic Encyclopedia of Bacteria and Archaea project I co-ran / run at the DOE JGI.

The ending is perfect
This is not the place to go into the specifies of which microbial genomes would be most useful. I would suggest, however, that a phylogenetic tree hang on the wall of every laboratory in which microbial genomes are being sequenced — for inspiration.
Somehow I had missed the crux of this paper until now.  I think it is worth reading by everyone out there working on microbes and/or their genomes.

Oh - and here is the compilation of Woese's papers I am making in Mendeley.

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