Jon Eisen – Genomic Encyclopedia of Bacteria and Archaea to sample the breadth of microbial diversity
I recently attended the 2010 American Society for Microbiology General Meeting with my colleague Mary Canady. I’ll be covered the scientific sessions and shared interesting developments in genetics, microbiology, and technology. See also the #ASMGM hashtag on twitter for conference tweets.
Jonathan Eisen spoke Tuesday on the Genomic Encyclopedia of Bacteria and Archaea, an ambitious project to sample across the breadth of microbial diversity and get a sense of just how much genetic diversity is represented across all bacteria. This project was undertaken to get a more balanced picture of genetic diversity, which is currently skewed in modern sequencing projects by under-representation of some groups. Genome sequence data has diverse uses including development of new antibiotics and drugs, as well as for the identification of new species, but without a big picture overview of the “Tree of Life“, scientists are very much like tourists in a strange city without a map, only finding the interesting stuff if they happen to stumble upon it.
Using a method based on an outline of this tree of life, Dr. Eisen was able to sequence species that covered the entire range of genetic diversity. They were then able to more easily analyze sequence data from environmental samples where the species in the sample are not known by essentially filling in the gaps in the branches. Once they had a means to estimate how genetically different one organism was from another, they could more easily discover novel proteins by intelligently selecting genetically distinct organisms and looking at the places where the sequences differed between the organisms.
Another area of research helped by the above framework is in sequencing of samples taken from nature in which novel organisms may be found. Often, many of the microbial species found in a sample don’t survive under the laboratory conditions necessary to grow enough of the bacteria for a sequencing project. These species then go undetected in the sample, unless you can predict something about the number and relationships of species in the initial mixed sample, so that you can tell that a certain genetic puzzle piece doesn’t fit with the known species in the sample. Dr. Eisen’s method aids this identification process by giving a framework for aligning gene sequences recoved from the sample against the known gene sequences of microorganisms, making the guesses about which genes belong to which organisms a little more certain.
Slides from Dr. Eisen’s talk are available at Slideshare.
[Disclosures: Dr. Gunn is a San Diego-based scientific consultant and academic community liaison for Mendeley. Former clients include a private single molecule sequencing startup.]