MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

Kang, Dongwan D.; Li, Feng; Kirton, Edward; Thomas, Ashleigh; Egan, Rob; An, Hong; Wang, Zhong

doi:10.7717/peerj.7359

Title: MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

Journal Article · 26 July 2019 · PeerJ

DOI: https://doi.org/10.7717/peerj.7359 · OSTI ID:1559796

Kang, Dongwan D. ^[1]; Li, Feng ^[2];

^[1];

^[1]; An, Hong ^[2];

^[3]

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of Science and Technology of China, Hefei (China)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California at Merced, Merced, CA (United States)

We previously reported on MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent analyses of uncultivated microbial species. MetaBAT has become one of the most popular binning tools largely due to its computational efficiency and ease of use, especially in binning experiments with a large number of samples and a large assembly. MetaBAT requires users to choose parameters to fine-tune its sensitivity and specificity. If those parameters are not chosen properly, binning accuracy can suffer, especially on assemblies of poor quality. Here, we developed MetaBAT 2 to overcome this problem. MetaBAT 2 uses a new adaptive binning algorithm to eliminate manual parameter tuning. We also performed extensive software engineering optimization to increase both computational and memory efficiency. Comparing MetaBAT 2 to alternative software tools on over 100 real world metagenome assemblies shows superior accuracy and computing speed. Binning a typical metagenome assembly takes only a few minutes on a single commodity workstation. We therefore recommend the community adopts MetaBAT 2 for their metagenome binning experiments. MetaBAT 2 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 Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1559796

Journal Information:: PeerJ, Journal Name: PeerJ Vol. 7; ISSN 2167-8359

Publisher:: PeerJ Inc.Copyright Statement

Country of Publication:: United States

Language:: English

References (43)

Salinimonas marina sp. nov. Isolated from Jeju Island Marine Sediment Kim, Minji; Lee, Ki-Eun; Cha, In-Tae Current Microbiology, Vol. 78, Issue 8 https://doi.org/10.1007/s00284-021-02576-9	journal	June 2021
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle Pasolli, Edoardo; Asnicar, Francesco; Manara, Serena Cell, Vol. 176, Issue 3 https://doi.org/10.1016/j.cell.2019.01.001	journal	January 2019
Ten years of next-generation sequencing technology van Dijk, Erwin L.; Auger, Hélène; Jaszczyszyn, Yan Trends in Genetics, Vol. 30, Issue 9 https://doi.org/10.1016/j.tig.2014.07.001	journal	September 2014
Metagenomics: DNA sequencing of environmental samples Tringe, Susannah Green; Rubin, Edward M. Nature Reviews Genetics, Vol. 6, Issue 11 https://doi.org/10.1038/nrg1709	journal	October 2005
A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.) Rinke, Christian; Rubino, Francesco; Messer, Lauren F. The ISME Journal, Vol. 13, Issue 3 https://doi.org/10.1038/s41396-018-0282-y	journal	October 2018
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria Nature Microbiology, Vol. 2, Issue 11 https://doi.org/10.1038/s41564-017-0012-7	journal	September 2017
Structure and function of the global topsoil microbiome Bahram, Mohammad; Hildebrand, Falk; Forslund, Sofia K. Nature, Vol. 560, Issue 7717 https://doi.org/10.1038/s41586-018-0386-6	journal	August 2018
Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes Lin, Hsin-Hung; Liao, Yu-Chieh Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep24175	journal	April 2016
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets Wu, Yu-Wei; Simmons, Blake A.; Singer, Steven W. Bioinformatics, Vol. 32, Issue 4 https://doi.org/10.1093/bioinformatics/btv638	journal	October 2015
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge Lu, Yang Young; Chen, Ting; Fuhrman, Jed A. Bioinformatics https://doi.org/10.1093/bioinformatics/btw290	journal	June 2016
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.955	journal	March 1997
IMG 4 version of the integrated microbial genomes comparative analysis system Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt963	journal	October 2013
metaSPAdes: a new versatile metagenomic assembler Nurk, Sergey; Meleshko, Dmitry; Korobeynikov, Anton Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.213959.116	journal	March 2017
Reconstructing single genomes from complex microbial communities Kang, Dongwan D.; Rubin, Edward M.; Wang, Zhong it - Information Technology, Vol. 58, Issue 3 https://doi.org/10.1515/itit-2016-0011	journal	January 2016
Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics software Alexander, Sczyrba,; Peter, Hofmann,; Peter, Belmann, ETH Zurich https://doi.org/10.3929/ethz-b-000206823	text	January 2017
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities Kang, Dongwan D.; Froula, Jeff; Egan, Rob PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1165	journal	January 2015
Diversity and composition of the North Sikkim hot spring mycobiome using a culture-independent method Das, Sayak; Roy, Goshaidas; Najar, Ishfaq Nabi Folia Microbiologica, Vol. 66, Issue 3 https://doi.org/10.1007/s12223-021-00859-z	journal	March 2021
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle Pasolli, Edoardo; Asnicar, Francesco; Manara, Serena Cell, Vol. 176, Issue 3 https://doi.org/10.1016/j.cell.2019.01.001	journal	January 2019
Ten years of next-generation sequencing technology van Dijk, Erwin L.; Auger, Hélène; Jaszczyszyn, Yan Trends in Genetics, Vol. 30, Issue 9 https://doi.org/10.1016/j.tig.2014.07.001	journal	September 2014
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas Nature Biotechnology, Vol. 35, Issue 8 https://doi.org/10.1038/nbt.3893	journal	August 2017
Binning metagenomic contigs by coverage and composition Alneberg, Johannes; Bjarnason, Brynjar Smári; de Bruijn, Ino Nature Methods, Vol. 11, Issue 11 https://doi.org/10.1038/nmeth.3103	journal	September 2014
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software Sczyrba, Alexander; Hofmann, Peter; Belmann, Peter Nature Methods, Vol. 14, Issue 11 https://doi.org/10.1038/nmeth.4458	journal	October 2017
Metagenomics: DNA sequencing of environmental samples Tringe, Susannah Green; Rubin, Edward M. Nature Reviews Genetics, Vol. 6, Issue 11 https://doi.org/10.1038/nrg1709	journal	October 2005
A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.) Rinke, Christian; Rubino, Francesco; Messer, Lauren F. The ISME Journal, Vol. 13, Issue 3 https://doi.org/10.1038/s41396-018-0282-y	journal	October 2018
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria Nature Microbiology, Vol. 2, Issue 11 https://doi.org/10.1038/s41564-017-0012-7	journal	September 2017
Structure and function of the global topsoil microbiome Bahram, Mohammad; Hildebrand, Falk; Forslund, Sofia K. Nature, Vol. 560, Issue 7717 https://doi.org/10.1038/s41586-018-0386-6	journal	August 2018
Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes Lin, Hsin-Hung; Liao, Yu-Chieh Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep24175	journal	April 2016
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets Wu, Yu-Wei; Simmons, Blake A.; Singer, Steven W. Bioinformatics, Vol. 32, Issue 4 https://doi.org/10.1093/bioinformatics/btv638	journal	October 2015
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge Lu, Yang Young; Chen, Ting; Fuhrman, Jed A. Bioinformatics https://doi.org/10.1093/bioinformatics/btw290	journal	June 2016
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.0955	journal	March 1997
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.955	journal	March 1997
IMG: the integrated microbial genomes database and comparative analysis system Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1044	journal	December 2011
IMG 4 version of the integrated microbial genomes comparative analysis system Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt963	journal	October 2013
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes Chen, I-Min A.; Chu, Ken; Palaniappan, Krishna Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky901	journal	October 2018
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
metaSPAdes: a new versatile metagenomic assembler Nurk, Sergey; Meleshko, Dmitry; Korobeynikov, Anton Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.213959.116	journal	March 2017
Improving contig binning of metagenomic data using d 2 S $$ {d}_2^S $$ oligonucleotide frequency dissimilarity Wang, Ying; Wang, Kun; Lu, Yang Young BMC Bioinformatics, Vol. 18, Issue 1 https://doi.org/10.1186/s12859-017-1835-1	journal	September 2017
Reconstructing single genomes from complex microbial communities Kang, Dongwan D.; Rubin, Edward M.; Wang, Zhong it - Information Technology, Vol. 58, Issue 3 https://doi.org/10.1515/itit-2016-0011	journal	January 2016
A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.) Rinke, Christian; Rubino, Francesco; Messer, Lauren Open Science Framework https://doi.org/10.17605/osf.io/paq3f	text	January 2018
The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures Strous, Marc; Kraft, Beate; Bisdorf, Regina Frontiers in Microbiology, Vol. 3 https://doi.org/10.3389/fmicb.2012.00410	journal	January 2012
Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics software Alexander, Sczyrba,; Peter, Hofmann,; Peter, Belmann, ETH Zurich https://doi.org/10.3929/ethz-b-000206823	text	January 2017
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities Kang, Dongwan D.; Froula, Jeff; Egan, Rob PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1165	journal	January 2015
BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation Graham, Elaina D.; Heidelberg, John F.; Tully, Benjamin J. PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3035	journal	January 2017

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Additional file 24 of MetaDecoder: a novel method for clustering metagenomic contigs Liu, Cong-Cong; Dong, Shan-Shan; Chen, Jia-Bin figshare https://doi.org/10.6084/m9.figshare.19342978.v1	dataset	January 2022
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Additional file 1 of Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line Wang, Kui; Gao, Peiwen; Geng, Lili figshare https://doi.org/10.6084/m9.figshare.20064686	dataset	January 2022
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Additional file 8 of Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line Wang, Kui; Gao, Peiwen; Geng, Lili figshare https://doi.org/10.6084/m9.figshare.20064710	dataset	January 2022
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Additional file 1 of Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity Behling, Anna H.; Wilson, Brooke C.; Ho, Daniel figshare https://doi.org/10.6084/m9.figshare.25210574	dataset	January 2024
Additional file 1 of Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies Feng, Xiaowen; Li, Heng figshare https://doi.org/10.6084/m9.figshare.25591343	dataset	January 2024
Additional file 1 of Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation Liew, Kok Jun; Shahar, Saleha; Shamsir, Mohd Shahir figshare https://doi.org/10.6084/m9.figshare.25754948	dataset	January 2024
Additional file 1 of Metagenomic insights into Heimdallarchaeia clades from the deep-sea cold seep and hydrothermal vent Liu, Rui; Cai, Ruining; Wang, Minxiao figshare https://doi.org/10.6084/m9.figshare.26085143.v1	dataset	January 2024
Additional file 1 of Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China Liang, Jie-Liang; Feng, Shi-wei; Jia, Pu figshare https://doi.org/10.6084/m9.figshare.26353256	dataset	January 2024
Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites Hervé, Vincent; Liu, Pengfei; Dietrich, Carsten PeerJ, Vol. 8 https://doi.org/10.7717/peerj.8614	journal	January 2020
From an extremophilic community to an electroautotrophic production strain: identifying a novel Knallgas bacterium as cathodic biofilm biocatalyst Reiner, Johannes Eberhard; Geiger, Katharina; Hackbarth, Max The ISME Journal, Vol. 14, Issue 5 https://doi.org/10.1038/s41396-020-0595-5	journal	January 2020
Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika Tran, Patricia Q.; Bachand, Samantha C.; McIntyre, Peter B. The ISME Journal, Vol. 15, Issue 7 https://doi.org/10.1038/s41396-021-00898-x	journal	February 2021
Binning unassembled short reads based on k-mer abundance covariance using sparse coding Kyrgyzov, Olexiy; Prost, Vincent; Gazut, Stéphane GigaScience, Vol. 9, Issue 4 https://doi.org/10.1093/gigascience/giaa028	journal	March 2020
Dynamic Genome Evolution and Blueprint of Complex Virocell Metabolism in Globally-Distributed Giant Viruses Moniruzzaman, Mohammad; Martinez-Gutierrez, Carolina A.; Weinheimer, Alaina R. https://doi.org/10.1101/836445	posted_content	January 2019
Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust Van Goethem, Marc W.; Swenson, Tami L.; Trubl, Gareth mBio, Vol. 10, Issue 6 https://doi.org/10.1128/mbio.02287-19	journal	December 2019
Metagenome-Assembled Genome Sequences of Five Strains from the Microtus ochrogaster (Prairie Vole) Fecal Microbiome Donovan, Meghan; Lynch, Michael D. J.; Mackey, Calvin S. Microbiology Resource Announcements, Vol. 9, Issue 2 https://doi.org/10.1128/mra.01310-19	journal	January 2020
Simulating metagenomic stable isotope probing datasets with MetaSIPSim Barnett, Samuel E.; Buckley, Daniel H. BMC Bioinformatics, Vol. 21, Issue 1 https://doi.org/10.1186/s12859-020-3372-6	journal	January 2020
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads Sanders, Jon G.; Nurk, Sergey; Salido, Rodolfo A. Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1834-9	journal	October 2019
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations Karcher, Nicolai; Pasolli, Edoardo; Asnicar, Francesco Genome Biology, Vol. 21, Issue 1 https://doi.org/10.1186/s13059-020-02042-y	journal	June 2020
A pipeline for targeted metagenomics of environmental bacteria Grieb, Anissa; Bowers, Robert M.; Oggerin, Monike Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-0790-7	journal	February 2020
Optimizing de novo genome assembly from PCR-amplified metagenomes Roux, Simon; Trubl, Gareth; Goudeau, Danielle PeerJ, Vol. 7 https://doi.org/10.7717/peerj.6902	journal	January 2019

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Title: MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

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