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

Lookup NU author(s): Professor Hans-Peter Klenk

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This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).


Abstract

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.


Publication metadata

Author(s): Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Paez-Espino D, Yoshikuni Y, Visel A, Whitman WB, Garrity GM, Eisen JA, Hugenholtz P, Pati A, Ivanova NN, Woyke T, Klenk HP, Kyrpides NC

Publication type: Article

Publication status: Published

Journal: Nature Biotechnology

Year: 2017

Volume: 35

Pages: 676-683

Online publication date: 12/06/2017

Acceptance date: 21/04/2017

ISSN (print): 1087-0156

ISSN (electronic): 1546-1696

Publisher: Nature Publishing Group

URL: https://doi.org/10.1038/nbt.3886

DOI: 10.1038/nbt.3886

PubMed id: 28604660


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