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.
- 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. doi: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. doi: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 = {2017},
month = {9}
}
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Figures / Tables:
Fig. 1: Assessment of genome quality. a, Estimated completeness and contamination of 7,903 genomes recovered from public metagenomes. Genome quality was defined as completeness − 5 × contamination, and only genomes with a quality of ≥ 50 were retained. Near-complete genomes (completeness ≥ 90%; contamination ≤ 5%) are shown inmore »
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- Medlar, Alan J.; Törönen, Petri; Holm, Liisa
- Nucleic Acids Research, Vol. 46, Issue W1
Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
journal, February 2018
- Stewart, Robert D.; Auffret, Marc D.; Warr, Amanda
- Nature Communications, Vol. 9, Issue 1
Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes
journal, October 2018
- Ahlgren, Nathan A.; Fuchsman, Clara A.; Rocap, Gabrielle
- The ISME Journal, Vol. 13, Issue 3
A human gut bacterial genome and culture collection for improved metagenomic analyses
journal, February 2019
- Forster, Samuel C.; Kumar, Nitin; Anonye, Blessing O.
- Nature Biotechnology, Vol. 37, Issue 2
Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean
journal, September 2018
- Martinez-Hernandez, Francisco; Fornas, Òscar; Lluesma Gomez, Monica
- The ISME Journal, Vol. 13, Issue 1
Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys
journal, June 2020
- Hou, Jialin; Sievert, Stefan M.; Wang, Yinzhao
- Microbiome, Vol. 8, Issue 1
MetaPOAP: presence or absence of metabolic pathways in metagenome-assembled genomes
journal, June 2018
- Ward, Lewis M.; Shih, Patrick M.; Fischer, Woodward W.
- Bioinformatics
Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family
journal, February 2019
- Lagkouvardos, Ilias; Lesker, Till R.; Hitch, Thomas C. A.
- 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
- Trosvik, Pål; de Muinck, Eric J.; Rueness, Eli K.
- Microbiome, Vol. 6, Issue 1
Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations
journal, March 2019
- Johri, Shaili; Doane, Michael; Allen, Lauren
- Diversity, Vol. 11, Issue 4
Chromulinavorax destructans, a pathogen of microzooplankton that provides a window into the enigmatic candidate phylum Dependentiae
journal, May 2019
- Deeg, Christoph M.; Zimmer, Matthias M.; George, Emma E.
- PLOS Pathogens, Vol. 15, Issue 5
The future of genomics in polar and alpine cyanobacteria
journal, February 2018
- Chrismas, Nathan A. M.; Anesio, Alexandre M.; Sánchez-Baracaldo, Patricia
- 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
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
- Brown, C. Titus; Moritz, Dominik; O’Brien, Michael P.
- Genome Biology, Vol. 21, Issue 1
Machine-Learning Classification Suggests That Many Alphaproteobacterial Prophages May Instead Be Gene Transfer Agents
journal, September 2019
- Kogay, Roman; Neely, Taylor B.; Birnbaum, Daniel P.
- Genome Biology and Evolution, Vol. 11, Issue 10
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
Heliorhodopsins are absent in diderm (Gram‐negative) bacteria: Some thoughts and possible implications for activity
journal, January 2019
- Flores‐Uribe, José; Hevroni, Gur; Ghai, Rohit
- Environmental Microbiology Reports, Vol. 11, Issue 3
The Who, Why, and How of Small-Molecule Production in Invertebrate Microbiomes: Basic Insights Fueling Drug Discovery
journal, March 2018
- Kwan, Jason C.
- mSystems, Vol. 3, Issue 2
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
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
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
journal, August 2018
- Parks, Donovan H.; Chuvochina, Maria; Waite, David W.
- Nature Biotechnology, Vol. 36, Issue 10
Contributions of single-cell genomics to our understanding of planktonic marine archaea
journal, October 2019
- Santoro, A. E.; Kellom, M.; Laperriere, S. M.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 374, Issue 1786
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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