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

Abstract

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.

Authors:
 [1];  [1];  [1];  [2]
+ Show Author Affiliations
  1. Department of Energy Joint Genome Institute, Walnut Creek, CA, (United States); ; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division
  2. 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)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1257449
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
PeerJ
Additional Journal Information:
Journal Volume: 3; Journal ID: ISSN 2167-8359
Publisher:
PeerJ Inc.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Metagenome binning; MetaBAT

Citation Formats

Kang, Dongwan D., Froula, Jeff, Egan, Rob, and Wang, Zhong. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. United States: N. p., 2015. Web. doi:10.7717/peerj.1165.
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Kang, Dongwan D., Froula, Jeff, Egan, Rob, & Wang, Zhong. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. United States. https://doi.org/10.7717/peerj.1165
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Kang, Dongwan D., Froula, Jeff, Egan, Rob, and Wang, Zhong. Thu . "MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities". United States. https://doi.org/10.7717/peerj.1165. https://www.osti.gov/servlets/purl/1257449.
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@article{osti_1257449,
title = {MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities},
author = {Kang, Dongwan D. and Froula, Jeff and Egan, Rob and Wang, Zhong},
abstractNote = {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.},
doi = {10.7717/peerj.1165},
journal = {PeerJ},
number = ,
volume = 3,
place = {United States},
year = {Thu Jan 01 00:00:00 EST 2015},
month = {Thu Jan 01 00:00:00 EST 2015}
}
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Journal Article:
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https://doi.org/10.7717/peerj.1165
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    Metagenome-Assembled Genome of USCα AHI, a Potential High-Affinity Methanotroph from Axel Heiberg Island, Canadian High Arctic
    journal, November 2019

    • Rusley, Calvin; Onstott, Tullis C.; Vishnivetskaya, Tatiana A.
    • Microbiology Resource Announcements, Vol. 8, Issue 46
    • DOI: 10.1128/mra.01178-19

    Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments
    journal, February 2019

    Trends of Microdiversity Reveal Depth-Dependent Evolutionary Strategies of Viruses in the Mediterranean
    journal, November 2019

    • Coutinho, Felipe Hernandes; Rosselli, Riccardo; Rodríguez-Valera, Francisco
    • mSystems, Vol. 4, Issue 6
    • DOI: 10.1128/msystems.00554-19

    MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage
    journal, November 2019

    A machine learning-based service for estimating quality of genomes using PATRIC
    journal, October 2019

    Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly
    journal, December 2019

    • Kang, Joyce B.; Siranosian, Benjamin A.; Moss, Eli L.
    • BMC Bioinformatics, Vol. 20, Issue S16
    • DOI: 10.1186/s12859-019-3073-1

    Simulating metagenomic stable isotope probing datasets with MetaSIPSim
    journal, January 2020

    A high-resolution genomic composition-based method with the ability to distinguish similar bacterial organisms
    journal, October 2019

    A completeness-independent method for pre-selection of closely related genomes for species delineation in prokaryotes
    journal, February 2020

    Long-term impact of fecal transplantation in healthy volunteers
    journal, December 2019

    • Goloshchapov, Oleg V.; Olekhnovich, Evgenii I.; Sidorenko, Sergey V.
    • BMC Microbiology, Vol. 19, Issue 1
    • DOI: 10.1186/s12866-019-1689-y

    Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake
    journal, August 2019

    Massive metagenomic data analysis using abundance-based machine learning
    journal, August 2019

    Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times
    journal, September 2018

    • Liang, Xiaoyu; Whitham, Jason M.; Holwerda, Evert K.
    • Biotechnology for Biofuels, Vol. 11, Issue 1
    • DOI: 10.1186/s13068-018-1238-1

    Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals
    journal, July 2016

    Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome
    journal, August 2017

    Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut
    journal, August 2019

    Impact of plants on the diversity and activity of methylotrophs in soil
    journal, March 2020

    Correction to: Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
    journal, March 2020

    Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture
    journal, January 2017

    • Driscoll, Connor B.; Otten, Timothy G.; Brown, Nathan M.
    • Standards in Genomic Sciences, Vol. 12, Issue 1
    • DOI: 10.1186/s40793-017-0224-8

    Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages
    journal, September 2019

    An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome
    text, January 2020

    Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients
    journal, February 2018

    • Gigliucci, Federica; von Meijenfeldt, F. A. Bastiaan; Knijn, Arnold
    • Frontiers in Cellular and Infection Microbiology, Vol. 8
    • DOI: 10.3389/fcimb.2018.00025

    MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins
    journal, August 2018

    An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs
    journal, October 2019

    Reads Binning Improves Alignment-Free Metagenome Comparison
    journal, November 2019

    Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract
    journal, June 2016

    • Laczny, Cedric C.; Muller, Emilie E. L.; Heintz-Buschart, Anna
    • Frontiers in Microbiology, Vol. 7
    • DOI: 10.3389/fmicb.2016.00884

    A Metagenomic Approach to Cyanobacterial Genomics
    journal, May 2017

    • Alvarenga, Danillo O.; Fiore, Marli F.; Varani, Alessandro M.
    • Frontiers in Microbiology, Vol. 8
    • DOI: 10.3389/fmicb.2017.00809

    Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems
    journal, October 2017

    Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea
    journal, December 2018

    Characterisation of the Carpinus betulus L. Phyllomicrobiome in Urban and Forest Areas
    journal, May 2019

    • Imperato, Valeria; Kowalkowski, Lukasz; Portillo-Estrada, Miguel
    • Frontiers in Microbiology, Vol. 10
    • DOI: 10.3389/fmicb.2019.01110

    Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome
    journal, March 2019

    Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations
    journal, June 2017

    • Miller, Ian; Chevrette, Marc; Kwan, Jason
    • Marine Drugs, Vol. 15, Issue 6
    • DOI: 10.3390/md15060165

    Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture
    journal, July 2018

    HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities
    journal, November 2017

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