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Title: Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

Author
item KYRPIDES, NIKOS - Joint Genome Institute
item HUGENHOLTZ, PHILIP - University Of Queensland
item EISEN, JONATHAN - University Of California
item WOYKE, TANJA - Joint Genome Institute
item GOKER, MARKUS - German Collection Of Microorganisms And Cell Cultures
item CHAIN, PATRICK - Los Alamos National Research Laboratory
item CHUN, JONGSIK - Seoul National University
item COLWELL, RITA - University Of Maryland
item DAWYNDT, PETER - Ghent University
item Labeda, David

Submitted to: PLoS Biology
Publication Type: Other
Publication Acceptance Date: 4/14/2014
Publication Date: 8/5/2014
Publication URL: http://handle.nal.usda.gov/10113/60423
Citation: Kyrpides, N.C., Hugenholtz, P., Eisen, J.A., Woyke, T., Goker, M., Chain, P.S., Chun, J., Colwell, R.R., Dawyndt, P., Labeda, D.P., et al. 2014. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biology. 12(8):e1001920.

Interpretive Summary: Microorganisms are important in sustaining life on Earth, but only a small fraction of total microbial diversity present on the planet has been isolated and characterized and an even smaller number of species have been characterized through genome sequencing. A genomic sequence catalogue of all known microbial species would provide an invaluable tool for understanding the microbial diversity of the planet, searching for novel genes and products, and for assessing the ongoing impact of global climate change.

Technical Abstract: Earth is a microbial planet. Microorganisms control and sustain all life on Earth. In terms of sheer numbers, they hold all the records: the most biomass, the most individuals, the greatest genetic diversity, and many others. They are our past-holding the secrets to the origins of life-and our future-sustaining life by maintaining essentially all of the biogeochemical cycles. For countering global warming, wastewater treatment, agricultural productivity and sustainability, disease control and human health, energy harvesting, biotechnology, and many other activities of critical importance, we heavily depend on cooperation with the microbial world. Yet, after 18 years of microbial genomics and with over 20,000 genome projects funded, we have only begun to scratch the surface of microbial diversity. While a significant number of microbial species have already been characterized in detail through genome sequencing, thus far we have covered less that 20% of the diversity of the cultured archaeal and bacterial species. Here we propose that a systematic effort to produce a comprehensive genomic catalogue of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently 11,000) should be funded. This effort will provide an unprecedented level of coverage of our planet’s genetic diversity, large-scale discovery of novel genes and functions, and the first step in an improved understanding of microbial evolution and the environment.