Simulating metagenomic stable isotope probing datasets with MetaSIPSim

Barnett, Samuel E.; Buckley, Daniel H.

doi:10.1186/s12859-020-3372-6

Title: Simulating metagenomic stable isotope probing datasets with MetaSIPSim

Journal Article · 29 January 2020 · BMC Bioinformatics

DOI: https://doi.org/10.1186/s12859-020-3372-6 · OSTI ID:1801593

Barnett, Samuel E. ^[1];

^[2]

Cornell Univ., Ithaca, NY (United States). School of Integrative Plant Science; OSTI
Cornell Univ., Ithaca, NY (United States). School of Integrative Plant Science

DNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific functions and improves the assembly and binning of these targeted genomes. However, empirical development of metagenomic-SIP methods is hindered by the complexity and cost of these studies. We developed a toolkit, ‘MetaSIPSim,’ to simulate sequencing read libraries for metagenomic-SIP experiments. MetaSIPSim is intended to generate datasets for method development and testing. To this end, we used MetaSIPSim generated data to demonstrate the advantages of metagenomic-SIP over a conventional shotgun metagenomic sequencing experiment. Through simulation we show that metagenomic-SIP improves the assembly and binning of isotopically labeled genomes relative to a conventional metagenomic approach. Improvements were dependent on experimental parameters and on sequencing depth. Community level G + C content impacted the assembly of labeled genomes and subsequent binning, where high community G + C generally reduced the benefits of metagenomic-SIP. Furthermore, when a high proportion of the community is isotopically labeled, the benefits of metagenomic-SIP decline. Finally, the choice of gradient fractions to sequence greatly influences method performance. Metagenomic-SIP is a valuable method for recovering isotopically labeled genomes from complex communities. We show that metagenomic-SIP performance depends on optimization of experimental parameters. MetaSIPSim allows for simulation of metagenomic-SIP datasets which facilitates the optimization and development of metagenomic-SIP experiments and analytical approaches for dealing with these data.

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Research Organization:: Cornell Univ., Ithaca, NY (United States)

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

Grant/Contract Number:: SC0004486; SC0016364

OSTI ID:: 1801593

Journal Information:: BMC Bioinformatics, Journal Name: BMC Bioinformatics Journal Issue: 1 Vol. 21; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (73)

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Plant roots alter microbial functional genes supporting root litter decomposition Shi, Shengjing; Herman, Donald J.; He, Zhili Soil Biology and Biochemistry, Vol. 127 https://doi.org/10.1016/j.soilbio.2018.09.013	journal	December 2018
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Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery Stewart, Robert D.; Auffret, Marc D.; Warr, Amanda Nature Biotechnology, Vol. 37, Issue 8 https://doi.org/10.1038/s41587-019-0202-3	journal	August 2019
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data Frank, J. A.; Pan, Y.; Tooming-Klunderud, A. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep25373	journal	May 2016
Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients: Quantitative analysis of SIP gradients Lueders, Tillmann; Manefield, Mike; Friedrich, Michael W. Environmental Microbiology, Vol. 6, Issue 1 https://doi.org/10.1046/j.1462-2920.2003.00536.x	journal	December 2003
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Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment: Necromass degradation in arctic marine sediment Müller, Albert L.; Pelikan, Claus; de Rezende, Julia R. Environmental Microbiology, Vol. 20, Issue 8 https://doi.org/10.1111/1462-2920.14297	journal	August 2018
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Use of Field-Based Stable Isotope Probing To Identify Adapted Populations and Track Carbon Flow through a Phenol-Degrading Soil Microbial Community DeRito, C. M.; Pumphrey, G. M.; Madsen, E. L. Applied and Environmental Microbiology, Vol. 71, Issue 12 https://doi.org/10.1128/aem.71.12.7858-7865.2005	journal	December 2005
RNA-Based Stable Isotope Probing and Isolation of Anaerobic Benzene-Degrading Bacteria from Gasoline-Contaminated Groundwater Kasai, Yuki; Takahata, Yoh; Manefield, Mike Applied and Environmental Microbiology, Vol. 72, Issue 5 https://doi.org/10.1128/aem.72.5.3586-3592.2006	journal	May 2006
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Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil Pepe-Ranney, Charles; Campbell, Ashley N.; Koechli, Chantal N. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00703	journal	May 2016
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MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies Kang, Dongwan D.; Li, Feng; Kirton, Edward PeerJ, Vol. 7 https://doi.org/10.7717/peerj.7359	journal	January 2019
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Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl Schildkraut, Carl L.; Marmur, Julius; Doty, Paul Journal of Molecular Biology, Vol. 4, Issue 6 https://doi.org/10.1016/S0022-2836(62)80100-4	journal	June 1962
Stable isotope probing in the metagenomics era: A bridge towards improved bioremediation Uhlik, Ondrej; Leewis, Mary-Cathrine; Strejcek, Michal Biotechnology Advances, Vol. 31, Issue 2 https://doi.org/10.1016/j.biotechadv.2012.09.003	journal	March 2013
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Stable-isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism Neufeld, Josh D.; Schäfer, Hendrik; Cox, Michael J. The ISME Journal, Vol. 1, Issue 6 https://doi.org/10.1038/ismej.2007.65	journal	August 2007
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Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil Thomas, François; Corre, Erwan; Cébron, Aurélie The ISME Journal, Vol. 13, Issue 7 https://doi.org/10.1038/s41396-019-0394-z	journal	March 2019
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Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery Stewart, Robert D.; Auffret, Marc D.; Warr, Amanda Nature Biotechnology, Vol. 37, Issue 8 https://doi.org/10.1038/s41587-019-0202-3	journal	August 2019
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data Frank, J. A.; Pan, Y.; Tooming-Klunderud, A. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep25373	journal	May 2016
Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients: Quantitative analysis of SIP gradients Lueders, Tillmann; Manefield, Mike; Friedrich, Michael W. Environmental Microbiology, Vol. 6, Issue 1 https://doi.org/10.1046/j.1462-2920.2003.00536.x	journal	December 2003
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Simulating Illumina metagenomic data with InSilicoSeq Gourlé, Hadrien; Karlsson-Lindsjö, Oskar; Hayer, Juliette Bioinformatics, Vol. 35, Issue 3 https://doi.org/10.1093/bioinformatics/bty630	journal	July 2018
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation O'Leary, Nuala A.; Wright, Mathew W.; Brister, J. Rodney Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1189	journal	November 2015
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Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment: Necromass degradation in arctic marine sediment Müller, Albert L.; Pelikan, Claus; de Rezende, Julia R. Environmental Microbiology, Vol. 20, Issue 8 https://doi.org/10.1111/1462-2920.14297	journal	August 2018
Use of Inorganic and Organic Nitrogen by Synechococcus spp. and Diatoms on the West Florida Shelf as Measured Using Stable Isotope Probing Wawrik, B.; Callaghan, A. V.; Bronk, D. A. Applied and Environmental Microbiology, Vol. 75, Issue 21 https://doi.org/10.1128/AEM.01002-09	journal	September 2009
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Stable Isotope Probing with 15N Achieved by Disentangling the Effects of Genome G+C Content and Isotope Enrichment on DNA Density Buckley, D. H.; Huangyutitham, V.; Hsu, S. -F. Applied and Environmental Microbiology, Vol. 73, Issue 10 https://doi.org/10.1128/AEM.02609-06	journal	March 2007
Stable Isotope Probing with 15N2 Reveals Novel Noncultivated Diazotrophs in Soil Buckley, D. H.; Huangyutitham, V.; Hsu, S. -F. Applied and Environmental Microbiology, Vol. 73, Issue 10 https://doi.org/10.1128/AEM.02610-06	journal	March 2007
Use of Field-Based Stable Isotope Probing To Identify Adapted Populations and Track Carbon Flow through a Phenol-Degrading Soil Microbial Community DeRito, C. M.; Pumphrey, G. M.; Madsen, E. L. Applied and Environmental Microbiology, Vol. 71, Issue 12 https://doi.org/10.1128/AEM.71.12.7858-7865.2005	journal	December 2005
RNA-Based Stable Isotope Probing and Isolation of Anaerobic Benzene-Degrading Bacteria from Gasoline-Contaminated Groundwater Kasai, Yuki; Takahata, Yoh; Manefield, Mike Applied and Environmental Microbiology, Vol. 72, Issue 5 https://doi.org/10.1128/AEM.72.5.3586-3592.2006	journal	May 2006
Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities Verastegui, Y.; Cheng, J.; Engel, K. mBio, Vol. 5, Issue 4 https://doi.org/10.1128/mBio.01157-14	journal	July 2014
Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil Pepe-Ranney, Charles; Campbell, Ashley N.; Koechli, Chantal N. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00703	journal	May 2016
SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments Youngblut, Nicholas D.; Barnett, Samuel E.; Buckley, Daniel H. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00570	journal	March 2018
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
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies Kang, Dongwan D.; Li, Feng; Kirton, Edward PeerJ, Vol. 7 https://doi.org/10.7717/peerj.7359	journal	January 2019

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
SIP
metagenomics
simulation
stable isotope probing

Additional file 1 of Simulating metagenomic stable isotope probing datasets with MetaSIPSim Barnett, Samuel; Buckley, Daniel https://doi.org/10.6084/m9.figshare.11775975 The current record is supplemented by this text	text	January 2020
Additional file 1 of Simulating metagenomic stable isotope probing datasets with MetaSIPSim Barnett, Samuel; Buckley, Daniel https://doi.org/10.6084/m9.figshare.11775975.v1 The current record is supplemented by this text	text	January 2020
Simulating metagenomic stable isotope probing datasets with MetaSIPSim Barnett, Samuel; Buckley, Daniel https://doi.org/10.6084/m9.figshare.c.4837992.v1 The current record is supplemented by this collection	collection	January 2020

Title: Simulating metagenomic stable isotope probing datasets with MetaSIPSim

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References (73)

Linked Research (3)

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