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

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.
Authors:
 [1] ;  [2] ;  [2] ;  [2] ; ORCiD logo [3] ; ORCiD logo [3] ;  [2] ;  [2] ; ORCiD logo [2] ; ORCiD logo [2] ;  [2] ; ORCiD logo [2] ;  [4] ;  [5] ;  [6] ; ORCiD logo [7] ;  [2] ;  [2] ;  [2] ;  [8] more »;  [2] « less
  1. Leibniz Inst. of German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. Leibniz Inst. of German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  4. Univ. of Georgia, Athens, GA (United States). Dept. of Microbiology
  5. Michigan State Univ., East Lansing, MI (United States). Dept. of Microbiology and Molecular Genetics; Namesforlife LLC, East Lansing, MI (United States)
  6. Univ. of California, Davis, CA (United States). Genome Center
  7. Univ. of Queensland, Brisbane (Australia). Australian Centre for Ecogenomics
  8. Newcastle Univ., Tyne (United Kingdom). School of Biology
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Accepted Manuscript
Journal Name:
Nature Biotechnology
Additional Journal Information:
Journal Volume: 35; Journal Issue: 7; Journal ID: ISSN 1087-0156
Publisher:
Springer Nature
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
archeal genomics; bacterial genomics; computational biology and bioinformatics; genomics; microbiology
OSTI Identifier:
1379902

Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J., Eloe-Fadrosh, Emiley A., Meier-Kolthoff, Jan P., Göker, Markus, Coates, R. Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A., Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B., Garrity, George M., Eisen, Jonathan A., Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N., Woyke, Tanja, Klenk, Hans-Peter, and Kyrpides, Nikos C.. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. United States: N. p., Web. doi:10.1038/nbt.3886.
Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J., Eloe-Fadrosh, Emiley A., Meier-Kolthoff, Jan P., Göker, Markus, Coates, R. Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A., Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B., Garrity, George M., Eisen, Jonathan A., Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N., Woyke, Tanja, Klenk, Hans-Peter, & Kyrpides, Nikos C.. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. United States. doi:10.1038/nbt.3886.
Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J., Eloe-Fadrosh, Emiley A., Meier-Kolthoff, Jan P., Göker, Markus, Coates, R. Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A., Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B., Garrity, George M., Eisen, Jonathan A., Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N., Woyke, Tanja, Klenk, Hans-Peter, and Kyrpides, Nikos C.. 2017. "1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life". United States. doi:10.1038/nbt.3886. https://www.osti.gov/servlets/purl/1379902.
@article{osti_1379902,
title = {1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life},
author = {Mukherjee, Supratim and Seshadri, Rekha and Varghese, Neha J. and Eloe-Fadrosh, Emiley A. and Meier-Kolthoff, Jan P. and Göker, Markus and Coates, R. Cameron and Hadjithomas, Michalis and Pavlopoulos, Georgios A. and Paez-Espino, David and Yoshikuni, Yasuo and Visel, Axel and Whitman, William B. and Garrity, George M. and Eisen, Jonathan A. and Hugenholtz, Philip and Pati, Amrita and Ivanova, Natalia N. and Woyke, Tanja and Klenk, Hans-Peter and Kyrpides, Nikos C.},
abstractNote = {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.},
doi = {10.1038/nbt.3886},
journal = {Nature Biotechnology},
number = 7,
volume = 35,
place = {United States},
year = {2017},
month = {6}
}

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Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass
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