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Title: 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:
ORCiD logo [1]; ORCiD logo [1];  [1];  [1];  [1];  [1]; ORCiD logo [1];  [1]
  1. 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. 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, and Tyson, Gene W. Mon . "Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life". United States. doi: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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Cited by: 244 works
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Figures / Tables:

Fig. 1 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 » red, medium-quality genomes (completeness ≥ 70%; contamination ≤ 10%) in blue, and partial genomes (completeness ≥ 50%; contamination ≤ 4%) in grey. Histograms along the x and y axes show the percentage of genomes at varying levels of completeness and contamination, respectively. Notably, only 171 of the 7,903 (2.2%) UBA genomes have > 5% contamination. b, Number of scaffolds comprising each of the 7,903 genomes with colours indicating genome quality. c, Number of tRNAs for each of the 20 standard amino acids identified within each of the 7,903 genomes with colours indicating genome quality.« less

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    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
    • DOI: 10.1093/gbe/evz206

    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
    • DOI: 10.1128/aem.00014-18

    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
    • DOI: 10.1111/1758-2229.12730

    Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach
    journal, February 2019


    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
    • DOI: 10.1038/nbt.4229

    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
    • DOI: 10.1098/rstb.2019.0096

    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
    • DOI: 10.1038/s41522-019-0090-9

      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.