Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Abstract
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by >30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.
- Authors:
-
- Univ. of Queensland (Australia)
- Publication Date:
- Research Org.:
- Univ. of Arizona, Tucson, AZ (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1500024
- Grant/Contract Number:
- SC0010580
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Microbiology
- Additional Journal Information:
- Journal Volume: 2; Journal Issue: 11; Journal ID: ISSN 2058-5276
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip, and Tyson, Gene W. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. United States: N. p., 2017.
Web. doi:10.1038/s41564-017-0012-7.
Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip, & Tyson, Gene W. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. United States. https://doi.org/10.1038/s41564-017-0012-7
Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip, and Tyson, Gene W. Mon .
"Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life". United States. https://doi.org/10.1038/s41564-017-0012-7. https://www.osti.gov/servlets/purl/1500024.
@article{osti_1500024,
title = {Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life},
author = {Parks, Donovan H. and Rinke, Christian and Chuvochina, Maria and Chaumeil, Pierre-Alain and Woodcroft, Ben J. and Evans, Paul N. and Hugenholtz, Philip and Tyson, Gene W.},
abstractNote = {Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by >30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.},
doi = {10.1038/s41564-017-0012-7},
journal = {Nature Microbiology},
number = 11,
volume = 2,
place = {United States},
year = {Mon Sep 11 00:00:00 EDT 2017},
month = {Mon Sep 11 00:00:00 EDT 2017}
}
Web of Science
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- Bioinformatics
Genomic and metagenomic insights into the microbial community of a thermal spring
journal, January 2019
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- Microbiome, Vol. 7, Issue 1
Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate
journal, May 2018
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- Microbiome, Vol. 6, Issue 1
Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations
journal, March 2019
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Chromulinavorax destructans, a pathogen of microzooplankton that provides a window into the enigmatic candidate phylum Dependentiae
journal, May 2019
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- PLOS Pathogens, Vol. 15, Issue 5
“
Candidatus
Colwellia aromaticivorans” sp. nov., “
Candidatus
Halocyntiibacter alkanivorans” sp. nov., and “
Candidatus
Ulvibacter alkanivorans” sp. nov. Genome Sequences
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- Microbiology Resource Announcements, Vol. 8, Issue 15
The future of genomics in polar and alpine cyanobacteria
journal, February 2018
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- FEMS Microbiology Ecology, Vol. 94, Issue 4
A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems
journal, July 2018
- Calusinska, Magdalena; Goux, Xavier; Fossépré, Marie
- Biotechnology for Biofuels, Vol. 11, Issue 1
Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep
journal, January 2019
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Gut Microbiome Dysbiosis and Immunometabolism: New Frontiers for Treatment of Metabolic Diseases
journal, December 2018
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- Mediators of Inflammation, Vol. 2018
The known and the unknown in soil microbial ecology
journal, January 2019
- Baldrian, Petr
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Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes
journal, July 2019
- Roux, Simon; Krupovic, Mart; Daly, Rebecca A.
- Nature Microbiology
Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity
journal, July 2020
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- Genome Biology, Vol. 21, Issue 1
A human gut bacterial genome and culture collection for improved metagenomic analyses
journal, February 2019
- Forster, Samuel C.; Kumar, Nitin; Anonye, Blessing O.
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Machine-Learning Classification Suggests That Many Alphaproteobacterial Prophages May Instead Be Gene Transfer Agents
journal, September 2019
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- Genome Biology and Evolution, Vol. 11, Issue 10
A census-based estimate of Earth's bacterial and archaeal diversity
journal, February 2019
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- PLOS Biology, Vol. 17, Issue 2
Alicycliphilus : current knowledge and potential for bioremediation of xenobiotics
journal, January 2019
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- Journal of Applied Microbiology, Vol. 126, Issue 6
Computational Framework for High-Quality Production and Large-Scale Evolutionary Analysis of Metagenome Assembled Genomes
journal, October 2019
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- Molecular Biology and Evolution, Vol. 37, Issue 2
Disinfection exhibits systematic impacts on the drinking water microbiome
journal, March 2020
- Dai, Zihan; Sevillano-Rivera, Maria C.; Calus, Szymon T.
- Microbiome, Vol. 8, Issue 1
How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?
journal, January 2018
- Rodriguez-R, Luis M.; Castro, Juan C.; Kyrpides, Nikos C.
- Applied and Environmental Microbiology, Vol. 84, Issue 6
Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status
journal, March 2020
- Jin, Yuan; Zhou, Jianglin; Zhou, Jing
- Biology Direct, Vol. 15, Issue 1
Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach
journal, February 2019
- Lambrechts, Sam; Willems, Anne; Tahon, Guillaume
- Frontiers in Microbiology, Vol. 10
Multiple levels of the unknown in microbiome research
journal, June 2019
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- BMC Biology, Vol. 17, Issue 1
metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics
journal, December 2020
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The distinction of CPR bacteria from other bacteria based on protein family content
journal, September 2019
- Méheust, Raphaël; Burstein, David; Castelle, Cindy J.
- Nature Communications, Vol. 10, Issue 1
Use of a Fluorescent Analog of Glucose (2-NBDG) To Identify Uncultured Rumen Bacteria That Take Up Glucose
journal, February 2019
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- Applied and Environmental Microbiology, Vol. 85, Issue 7
Identification of Molecular Markers That Are Specific to the Class Thermoleophilia
journal, May 2019
- Hu, Danyu; Zang, Yang; Mao, Yingjin
- Frontiers in Microbiology, Vol. 10
Primer-free FISH probes from metagenomics/metatranscriptomics data permit the study of uncharacterised taxa in complex microbial communities
journal, June 2019
- Tan, Shi Ming; Yung, Pui Yi Maria; Hutchinson, Paul E.
- npj Biofilms and Microbiomes, Vol. 5, Issue 1
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