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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]
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  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.
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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
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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.
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@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}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1038/s41564-017-0012-7
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Cited by: 771 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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