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Nat Biotechnol. 2017 Jul;35(7):676-683. doi: 10.1038/nbt.3886. Epub 2017 Jun 12.

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.

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Department of Energy, Joint Genome Institute, Walnut Creek, California, USA.
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Department of Microbiology, University of Georgia, Athens, Georgia, USA.
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA.
NamesforLife, LLC, East Lansing, Michigan, USA.
University of California Davis Genome Center, Davis, California, USA.
Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia.
School of Biology, Newcastle University, Newcastle upon, Tyne, UK.


We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.

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