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

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.

doi:10.1038/nbt.3886

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

Journal Article · Mon Jun 12 00:00:00 EDT 2017 · Nature Biotechnology

DOI:https://doi.org/10.1038/nbt.3886· OSTI ID:1379902

Mukherjee, Supratim ^[1]; Seshadri, Rekha ^[2]; Varghese, Neha J. ^[2]; Eloe-Fadrosh, Emiley A. ^[2];

^[3];

^[3]; Coates, R. Cameron ^[2]; Hadjithomas, Michalis ^[2];

^[2];

^[2]; Yoshikuni, Yasuo ^[2];

^[2]; Whitman, William B. ^[4]; Garrity, George M. ^[5]; Eisen, Jonathan A. ^[6];

^[7]; Pati, Amrita ^[2]; Ivanova, Natalia N. ^[2]; Woyke, Tanja ^[2]; Klenk, Hans-Peter ^[8] more »

Leibniz Inst. of German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Leibniz Inst. of German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
Univ. of Georgia, Athens, GA (United States). Dept. of Microbiology
Michigan State Univ., East Lansing, MI (United States). Dept. of Microbiology and Molecular Genetics; Namesforlife LLC, East Lansing, MI (United States)
Univ. of California, Davis, CA (United States). Genome Center
Univ. of Queensland, Brisbane (Australia). Australian Centre for Ecogenomics
Newcastle Univ., Tyne (United Kingdom). School of Biology

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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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1379902

Journal Information:: Nature Biotechnology, Vol. 35, Issue 7; ISSN 1087-0156

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 141 works

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Comprehensive functional characterization of the glycoside hydrolase family 3 enzymes from Cellvibrio japonicus reveals unique metabolic roles in biomass saccharification : Complex glucan utilization in Nelson, Cassandra E.; Attia, Mohamed A.; Rogowski, Artur Environmental Microbiology, Vol. 19, Issue 12 https://doi.org/10.1111/1462-2920.13959	journal	December 2017
Detecting signatures of a sponge-associated lifestyle in bacterial genomes: Sponge-associated lifestyle in bacterial genomes Díez-Vives, Cristina; Esteves, Ana I. S.; Costa, Rodrigo Environmental Microbiology Reports, Vol. 10, Issue 4 https://doi.org/10.1111/1758-2229.12655	journal	July 2018
A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index Barco, R. A.; Garrity, G. M.; Scott, J. J. mBio, Vol. 11, Issue 1 https://doi.org/10.1128/mbio.02475-19	journal	January 2020
Draft Genome Sequences of Seven Chryseobacterium Type Strains Matu, Andisiwe; Lum Nde, Adeline; Oosthuizen, Lize Microbiology Resource Announcements, Vol. 8, Issue 1 https://doi.org/10.1128/mra.01518-18	journal	January 2019
Critical Assessment of Metagenome Interpretation Enters the Second Round Bremges, Andreas; McHardy, Alice C. mSystems, Vol. 3, Issue 4 https://doi.org/10.1128/msystems.00103-18	journal	July 2018
Unique Patterns and Biogeochemical Relevance of Two-Component Sensing in Marine Bacteria Held, Noelle A.; McIlvin, Matthew R.; Moran, Dawn M. mSystems, Vol. 4, Issue 1 https://doi.org/10.1128/msystems.00317-18	journal	February 2019
eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria Kono, Nobuaki; Tomita, Masaru; Arakawa, Kazuharu BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-017-4162-z	journal	October 2017
Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains Acuña-Amador, Luis; Primot, Aline; Cadieu, Edouard BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-017-4429-4	journal	January 2018
Comparative genomics of Bacteria commonly identified in the built environment Merino, Nancy; Zhang, Shu; Tomita, Masaru BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-018-5389-z	journal	January 2019
Antibacterial and anticancer activities of orphan biosynthetic gene clusters from Atlantis II Red Sea brine pool Ziko, Laila; Saqr, Al-Hussein A.; Ouf, Amged Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1103-3	journal	March 2019
Metagenomic reconstructions of gut microbial metabolism in weanling pigs Wang, Weilan; Hu, Huifeng; Zijlstra, Ruurd T. Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0662-1	journal	March 2019
Genome-Based Taxonomic Classification of the Phylum Actinobacteria Nouioui, Imen; Carro, Lorena; García-López, Marina Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02007	journal	August 2018
Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes García-López, Marina; Meier-Kolthoff, Jan P.; Tindall, Brian J. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02083	journal	September 2019
Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application Oh, Changsuk; Kim, T. Doohun; Kim, Kyeong Kyu Crystals, Vol. 9, Issue 11 https://doi.org/10.3390/cryst9110597	journal	November 2019
Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods Bingol, Kerem High-Throughput, Vol. 7, Issue 2 https://doi.org/10.3390/ht7020009	journal	April 2018
Comparison of Phylogenetic Tree Topologies for Nitrogen Associated Genes Partially Reconstruct the Evolutionary History of Saccharomyces cerevisiae Villalobos-Cid, Manuel; Salinas, Francisco; Kessi-Pérez, Eduardo I. Microorganisms, Vol. 8, Issue 1 https://doi.org/10.3390/microorganisms8010032	journal	December 2019
CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria Wang, Gaoyan; Zhao, Zhiying; Ke, Jing Nature Microbiology, Vol. 4, Issue 12 https://doi.org/10.1038/s41564-019-0573-8	journal	October 2019
CAMITAX: Taxon labels for microbial genomes Bremges, Andreas; Fritz, Adrian; McHardy, Alice C. GigaScience, Vol. 9, Issue 1 https://doi.org/10.1093/gigascience/giz154	journal	January 2020
Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis Porter, Teresita M.; Hajibabaei, Mehrdad Molecular Ecology, Vol. 27, Issue 2 https://doi.org/10.1111/mec.14478	journal	January 2018
Excisionase in Pf filamentous prophage controls lysis‐lysogeny decision‐making in Pseudomonas aeruginosa Li, Yangmei; Liu, Xiaoxiao; Tang, Kaihao Molecular Microbiology, Vol. 111, Issue 2 https://doi.org/10.1111/mmi.14170	journal	December 2018
A global atlas of the dominant bacteria found in soil Delgado-Baquerizo, Manuel; Oliverio, Angela M.; Brewer, Tess E. Science, Vol. 359, Issue 6373 https://doi.org/10.1126/science.aap9516	journal	January 2018
Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate Trosvik, Pål; de Muinck, Eric J.; Rueness, Eli K. Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0468-6	journal	May 2018
Cyanobacteria and Alphaproteobacteria May Facilitate Cooperative Interactions in Niche Communities Van Goethem, Marc W.; Makhalanyane, Thulani P.; Cowan, Don A. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02099	journal	October 2017
Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order Methylococcales) Calls for the Reclassification of Members at the Genus and Species Levels Orata, Fabini D.; Meier-Kolthoff, Jan P.; Sauvageau, Dominic Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.03162	journal	December 2018
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria Nature Microbiology, Vol. 2, Issue 11 https://doi.org/10.1038/s41564-017-0012-7	journal	September 2017
High-quality draft genome sequences of Pseudomonas monteilii DSM 14164T, Pseudomonas mosselii DSM 17497T, Pseudomonas plecoglossicida DSM 15088T, Pseudomonas taiwanensis DSM 21245T and Pseudomonas vranovensis DSM 16006T: taxonomic considerations Peña, Arantxa; Busquets, Antonio; Gomila, Margarita Access Microbiology, Vol. 1, Issue 10 https://doi.org/10.1099/acmi.0.000067	journal	December 2019
Genome‐based evolutionary history of Pseudomonas spp Hesse, Cedar; Schulz, Frederik; Bull, Carolee T. Environmental Microbiology, Vol. 20, Issue 6 https://doi.org/10.1111/1462-2920.14130	journal	June 2018
A review of computational tools for design and reconstruction of metabolic pathways Wang, Lin; Dash, Satyakam; Ng, Chiam Yu Synthetic and Systems Biotechnology, Vol. 2, Issue 4 https://doi.org/10.1016/j.synbio.2017.11.002	journal	December 2017
The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species Wu, Linhuan; McCluskey, Kevin; Desmeth, Philippe GigaScience, Vol. 7, Issue 5 https://doi.org/10.1093/gigascience/giy026	journal	March 2018
Establishment of recombineering genome editing system in Paraburkholderia megapolitana empowers activation of silent biosynthetic gene clusters Zheng, Wentao; Wang, Xue; Zhou, Haibo Microbial Biotechnology, Vol. 13, Issue 2 https://doi.org/10.1111/1751-7915.13535	journal	February 2020
Draft Genome Sequence of Rubricoccus marinus SG-29 ^T , a Marine Bacterium within the Family Rhodothermaceae , Which Contains Two Different Rhodopsin Genes Nakajima, Yu; Yoshizawa, Susumu; Park, Sanghwa Genome Announcements, Vol. 5, Issue 38 https://doi.org/10.1128/genomea.00990-17	journal	September 2017
Genomic Variations Underlying Speciation and Niche Specialization of Shewanella baltica Deng, Jie; Auchtung, Jennifer M.; Konstantinidis, Konstantinos T. mSystems, Vol. 4, Issue 5 https://doi.org/10.1128/msystems.00560-19	journal	October 2019
Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence Yassin, Atteyet F.; Langenberg, Stefan; Huntemann, Marcel PLOS ONE, Vol. 12, Issue 12 https://doi.org/10.1371/journal.pone.0188914	journal	December 2017
The Composite 259-kb Plasmid of Martelella mediterranea DSM 17316T–A Natural Replicon with Functional RepABC Modules from Rhodobacteraceae and Rhizobiaceae Bartling, Pascal; Brinkmann, Henner; Bunk, Boyke Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01787	journal	September 2017
Commentary: Genome-Based Taxonomic Classification of the Phylum Actinobacteria Gupta, Radhey S. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00206	journal	February 2019
Identification of Molecular Markers That Are Specific to the Class Thermoleophilia Hu, Danyu; Zang, Yang; Mao, Yingjin Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01185	journal	May 2019

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