Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria; Chaumeil, Pierre-Alain; Woodcroft, Ben J.; Evans, Paul N.; Hugenholtz, Philip; Tyson, Gene W.

doi:10.1038/s41564-017-0012-7

Title: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Journal Article · Mon Sep 11 00:00:00 EDT 2017 · Nature Microbiology

DOI:https://doi.org/10.1038/s41564-017-0012-7· OSTI ID:1500024

^[1];

^[1]; Chuvochina, Maria ^[1]; Chaumeil, Pierre-Alain ^[1]; Woodcroft, Ben J. ^[1]; Evans, Paul N. ^[1];

^[1]; Tyson, Gene W. ^[1]

Univ. of Queensland (Australia)

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.

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Research Organization:: Univ. of Arizona, Tucson, AZ (United States)

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

Grant/Contract Number:: SC0010580

OSTI ID:: 1500024

Journal Information:: Nature Microbiology, Vol. 2, Issue 11; ISSN 2058-5276

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 771 works

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Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi Boyd, Joel A.; Jungbluth, Sean P.; Leu, Andy O. The ISME Journal, Vol. 13, Issue 5 https://doi.org/10.1038/s41396-018-0343-2	journal	January 2019
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
International Committee on Systematics of Prokaryotes (ICSP) Subcommittee on the taxonomy of Chlamydiae. Minutes of the closed meeting, 20 March 2019, Seattle, WA, USA Borel, Nicole; Horn, Matthias; Greub, Gilbert International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 11 https://doi.org/10.1099/ijsem.0.003738	journal	November 2019
Shotgun metagenomics of honey DNA: Evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature Bovo, Samuele; Ribani, Anisa; Utzeri, Valerio Joe PLOS ONE, Vol. 13, Issue 10 https://doi.org/10.1371/journal.pone.0205575	journal	October 2018
Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment Shen, Liang; Liu, Yongqin; Wang, Ninglian Microorganisms, Vol. 7, Issue 7 https://doi.org/10.3390/microorganisms7070211	journal	July 2019
AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination Medlar, Alan J.; Törönen, Petri; Holm, Liisa Nucleic Acids Research, Vol. 46, Issue W1 https://doi.org/10.1093/nar/gky359	journal	May 2018
Genome-centric view of carbon processing in thawing permafrost Woodcroft, Ben J.; Singleton, Caitlin M.; Boyd, Joel A. Nature, Vol. 560, Issue 7716 https://doi.org/10.1038/s41586-018-0338-1	journal	July 2018
Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean Martinez-Hernandez, Francisco; Fornas, Òscar; Lluesma Gomez, Monica The ISME Journal, Vol. 13, Issue 1 https://doi.org/10.1038/s41396-018-0278-7	journal	September 2018
MetaPOAP: presence or absence of metabolic pathways in metagenome-assembled genomes Ward, Lewis M.; Shih, Patrick M.; Fischer, Woodward W. Bioinformatics https://doi.org/10.1093/bioinformatics/bty510	journal	June 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
Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations Johri, Shaili; Doane, Michael; Allen, Lauren Diversity, Vol. 11, Issue 4 https://doi.org/10.3390/d11040049	journal	March 2019
Chromulinavorax destructans, a pathogen of microzooplankton that provides a window into the enigmatic candidate phylum Dependentiae Deeg, Christoph M.; Zimmer, Matthias M.; George, Emma E. PLOS Pathogens, Vol. 15, Issue 5 https://doi.org/10.1371/journal.ppat.1007801	journal	May 2019
“ Candidatus Colwellia aromaticivorans” sp. nov., “ Candidatus Halocyntiibacter alkanivorans” sp. nov., and “ Candidatus Ulvibacter alkanivorans” sp. nov. Genome Sequences Campeão, Mariana E.; Swings, Jean; Silva, Bruno Sergio Microbiology Resource Announcements, Vol. 8, Issue 15 https://doi.org/10.1128/mra.00086-19	journal	April 2019
The future of genomics in polar and alpine cyanobacteria Chrismas, Nathan A. M.; Anesio, Alexandre M.; Sánchez-Baracaldo, Patricia FEMS Microbiology Ecology, Vol. 94, Issue 4 https://doi.org/10.1093/femsec/fiy032	journal	February 2018
The known and the unknown in soil microbial ecology Baldrian, Petr FEMS Microbiology Ecology, Vol. 95, Issue 2 https://doi.org/10.1093/femsec/fiz005	journal	January 2019
Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity Brown, C. Titus; Moritz, Dominik; O’Brien, Michael P. Genome Biology, Vol. 21, Issue 1 https://doi.org/10.1186/s13059-020-02066-4	journal	July 2020
Machine-Learning Classification Suggests That Many Alphaproteobacterial Prophages May Instead Be Gene Transfer Agents Kogay, Roman; Neely, Taylor B.; Birnbaum, Daniel P. Genome Biology and Evolution, Vol. 11, Issue 10 https://doi.org/10.1093/gbe/evz206	journal	September 2019
Alicycliphilus : current knowledge and potential for bioremediation of xenobiotics Solís‐González, C. J.; Loza‐Tavera, H. Journal of Applied Microbiology, Vol. 126, Issue 6 https://doi.org/10.1111/jam.14207	journal	January 2019
Computational Framework for High-Quality Production and Large-Scale Evolutionary Analysis of Metagenome Assembled Genomes Murovec, Boštjan; Deutsch, Leon; Stres, Blaz Molecular Biology and Evolution, Vol. 37, Issue 2 https://doi.org/10.1093/molbev/msz237	journal	October 2019
How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity? Rodriguez-R, Luis M.; Castro, Juan C.; Kyrpides, Nikos C. Applied and Environmental Microbiology, Vol. 84, Issue 6 https://doi.org/10.1128/aem.00014-18	journal	January 2018
Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach Lambrechts, Sam; Willems, Anne; Tahon, Guillaume Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00242	journal	February 2019
metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics Laso-Jadart, Romuald; Ambroise, Christophe; Peterlongo, Pierre PLOS ONE, Vol. 15, Issue 12 https://doi.org/10.1371/journal.pone.0244637	journal	December 2020
Use of a Fluorescent Analog of Glucose (2-NBDG) To Identify Uncultured Rumen Bacteria That Take Up Glucose Tao, Junyi; McCourt, Courtney; Sultana, Halima Applied and Environmental Microbiology, Vol. 85, Issue 7 https://doi.org/10.1128/aem.03018-18	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