Exploring standards to advance microbia...( WALNUT CREEK CA -- Microbes contribut...)

WALNUT CREEK, CA -- Microbes contribute to manifold human endeavors ranging from bioenergy to agriculture to medicine. Moreover, they make the Earth's biogeochemical cycles go round, a prerequisite for all life on the planet. Exceedingly numerous, they are also extremely diverse, encompassing most of Earth's total biodiversity. So it should come as no surprise to find that two-thirds of the nearly 5,000 genome projects reported in the Genomes OnLine Database (http://www.genomesonline.org) involve microbes. But far more could be done with microbial genomics, according to DOE JGI Genome Biology head Nikos Kyrpides, if researchers would embrace the world of possibilities that lie beyond the present anthropocentric focus and would also institute shared standards for genomic data collection and analysis.

In a perspective piece published in the July issue of the journal Nature Biotechnology, Kyrpides reflects on the role of microbial studies in the genomics revolution of the past decade, and considers the factors that have hindered the advancement of the field. Although nearly 1,000 microbial genomes have been sequenced over the past 15 years, nearly a quarter of them by DOE JGI, he noted that the data obtained has been compromised by the lack of standards for so many critical procedures in the field, procedures ranging from simple data exchange to gene finding, function prediction, and metabolic pathway description. Echoing other researchers, most notably DOE JGI's Patrick Chain and Miriam Land during the recent "Sequencing, Finishing, Analysis in the Future" Conference, Kyrpides calls for the development of genome annotation standards and their adoption by sequencing centers around the world a necessity for meaningful genome comparisons.

Kyrpides offers numerous suggestions to meet these and other challenges that face genomics research in the decade ahead. For example, the list of microbial genomes for p
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