MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

Kang, Dongwan D.; Froula, Jeff; Egan, Rob; Wang, Zhong

doi:10.7717/peerj.1165

Title: MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

Journal Article · Thu Jan 01 00:00:00 EST 2015 · PeerJ

DOI:https://doi.org/10.7717/peerj.1165· OSTI ID:1257449

Kang, Dongwan D. ^[1]; Froula, Jeff ^[1]; Egan, Rob ^[1]; Wang, Zhong ^[2]

Department of Energy Joint Genome Institute, Walnut Creek, CA, (United States); ; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division
Department of Energy Joint Genome Institute, Walnut Creek, CA, (United States); ; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division; Univ. of California, Merced, CA (United States)

Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because of the complex nature of these communities, existing metagenome binning methods often miss a large number of microbial species. In addition, most of the tools are not scalable to large datasets. Here we introduce automated software called MetaBAT that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency for accurate metagenome binning. MetaBAT outperforms alternative methods in accuracy and computational efficiency on both synthetic and real metagenome datasets. Lastly, it automatically forms hundreds of high quality genome bins on a very large assembly consisting millions of contigs in a matter of hours on a single node. MetaBAT is open source software and available at https://bitbucket.org/berkeleylab/metabat.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1257449

Journal Information:: PeerJ, Vol. 3; ISSN 2167-8359

Publisher:: PeerJ Inc.Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 990 works

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Tracking microbial evolution in the human gut using Hi-C Yaffe, Eitan; Relman, David A. Nature Microbiology https://doi.org/10.1101/594903	journal	March 2019
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Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths Johnston, Eric R.; Hatt, Janet K.; He, Zhili Proceedings of the National Academy of Sciences, Vol. 116, Issue 30 https://doi.org/10.1073/pnas.1901307116	journal	July 2019
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Novel autotrophic organisms contribute significantly to the internal carbon cycling potential of a boreal lake Peura, Sari; Buck, Moritz; Aalto, Sanni L. mBio https://doi.org/10.1101/309633	journal	April 2018
Comparative Genomics Guides Elucidation of Vitamin B ₁₂ Biosynthesis in Novel Human-Associated Akkermansia Strains Kirmiz, Nina; Galindo, Kadir; Cross, Karissa L. Applied and Environmental Microbiology, Vol. 86, Issue 3 https://doi.org/10.1128/aem.02117-19	journal	January 2020
Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota Zhang, Shan; Song, Weizhi; Wemheuer, Bernd mSystems, Vol. 4, Issue 4 https://doi.org/10.1128/msystems.00288-19	journal	August 2019
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KBase Silver Case Study: Determining Media Formulation Requirements for Isolation of Microbiome Constituents Whitham, Jason North Carolina State University https://doi.org/10.25982/68579.143/1766297	dataset	January 2021
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Highlighting Clinical Metagenomics for Enhanced Diagnostic Decision-making: A Step Towards Wider Implementation Forbes, Jessica D.; Knox, Natalie C.; Peterson, Christy-Lynn Computational and Structural Biotechnology Journal, Vol. 16 https://doi.org/10.1016/j.csbj.2018.02.006	journal	January 2018
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Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome Zhang, Yunzeng; Xu, Jin; Riera, Nadia Microbiome, Vol. 5, Issue 1 https://doi.org/10.1186/s40168-017-0304-4	journal	August 2017
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Metagenomics Reveals Microbial Diversity and Metabolic Potentials of Seawater and Surface Sediment From a Hadal Biosphere at the Yap Trench Zhang, Xinxu; Xu, Wei; Liu, Yang Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02402	journal	October 2018
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Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures Thomas, Scott C.; Tamadonfar, Kevin O.; Seymour, Cale O. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01427	journal	July 2019
Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture Toth, Courtney; Berdugo-Clavijo, Carolina; O’Farrell, Corynne Microorganisms, Vol. 6, Issue 3 https://doi.org/10.3390/microorganisms6030065	journal	July 2018
HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities Song, Weizhi; Steensen, Kerrin; Thomas, Torsten PeerJ, Vol. 5 https://doi.org/10.7717/peerj.4015	journal	November 2017

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