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Exploring standards to advance microbial genomics
Date:7/10/2009

otential sequencing, limited to the approximately one percent of the organisms that can be cultured in the lab, has been further biased by a focus on a few groups of particular impact on human health or activities. Thus, vast realms of biodiversity remain unexplored. Kyrpides applauds the effort to coordinate balanced sampling of the Tree of Life recently launched through GEBA: the Genomic Encyclopedia of Bacteria and Archaea (http://www.jgi.doe.gov/programs/GEBA/index.html). He also sees a way forward using single-cell genomics ⎯ a technique now being pursued in earnest by DOE JGI researcher Tanja Woyke and her colleagues ⎯ in partnership with environmental metagenomics to provide a more holistic understanding of microbial communities and their individual members.

Kyrpides also suggests several innovative approaches for easing the data processing bottleneck accompanying the exponential increase in genomic data. All-versus-all gene comparisons previously a common practice will become infeasible. To reduce the size of the datasets, he proposes a proxy approach in which one protein from each protein family or one species from each genus represents the group. Taking this one step farther, all the genes from all the sequenced strains in a species the pan-genome for that species would constitute the genome representing that species for gene comparisons.

Sharing his vision for the future of microbial genomics, Kyrpides observes: "The remarkable number of microbes⎯already estimated to be several orders of magnitude greater than the number of stars in the universe⎯urgently calls for a transition from random, anecdotal, and small scale surveys towards a systematic and comprehensive exploration of our planet." With new tools in hand and international initiatives for increased collaboration underway, the field of microbial genomics is poised for a decade of exciting advances. '/>"/>

Contact: David Gilbert
degilbert@lbl.gov
925-296-5643
DOE/Joint Genome Institute
Source:Eurekalert  

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