SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments
Abstract
DNA Stable isotope probing (DNA-SIP) is a powerful method that links identity to function within microbial communities. The combination of DNA-SIP with multiplexed high throughput DNA sequencing enables simultaneous mapping of in situ assimilation dynamics for thousands of microbial taxonomic units. Hence, high throughput sequencing enabled SIP has enormous potential to reveal patterns of carbon and nitrogen exchange within microbial food webs. There are several different methods for analyzing DNA-SIP data and despite the power of SIP experiments, it remains difficult to comprehensively evaluate method accuracy across a wide range of experimental parameters. We have developed a toolset (SIPSim) that simulates DNA-SIP data, and we use this toolset to systematically evaluate different methods for analyzing DNA-SIP data. Specifically, we employ SIPSim to evaluate the effects that key experimental parameters (e.g., level of isotopic enrichment, number of labeled taxa, relative abundance of labeled taxa, community richness, community evenness, and beta-diversity) have on the specificity, sensitivity, and balanced accuracy (defined as the product of specificity and sensitivity) of DNA-SIP analyses. Furthermore, SIPSim can predict analytical accuracy and power as a function of experimental design and community characteristics, and thus should be of great use in the design and interpretation of DNA-SIP experiments.
- Authors:
-
- Cornell Univ., Ithaca, NY (United States)
- Publication Date:
- Research Org.:
- Cornell Univ., Ithaca, NY (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1510497
- Alternate Identifier(s):
- OSTI ID: 1864327
- Grant/Contract Number:
- SC0004486; SC0010558; SC0016364
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 9; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; DNA-SIP; SIP; method; microbial; community; function; SIPSim
Citation Formats
Youngblut, Nicholas D., Barnett, Samuel E., and Buckley, Daniel H. SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments. United States: N. p., 2018.
Web. doi:10.3389/fmicb.2018.00570.
Youngblut, Nicholas D., Barnett, Samuel E., & Buckley, Daniel H. SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments. United States. https://doi.org/10.3389/fmicb.2018.00570
Youngblut, Nicholas D., Barnett, Samuel E., and Buckley, Daniel H. 2018.
"SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments". United States. https://doi.org/10.3389/fmicb.2018.00570. https://www.osti.gov/servlets/purl/1510497.
@article{osti_1510497,
title = {SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments},
author = {Youngblut, Nicholas D. and Barnett, Samuel E. and Buckley, Daniel H.},
abstractNote = {DNA Stable isotope probing (DNA-SIP) is a powerful method that links identity to function within microbial communities. The combination of DNA-SIP with multiplexed high throughput DNA sequencing enables simultaneous mapping of in situ assimilation dynamics for thousands of microbial taxonomic units. Hence, high throughput sequencing enabled SIP has enormous potential to reveal patterns of carbon and nitrogen exchange within microbial food webs. There are several different methods for analyzing DNA-SIP data and despite the power of SIP experiments, it remains difficult to comprehensively evaluate method accuracy across a wide range of experimental parameters. We have developed a toolset (SIPSim) that simulates DNA-SIP data, and we use this toolset to systematically evaluate different methods for analyzing DNA-SIP data. Specifically, we employ SIPSim to evaluate the effects that key experimental parameters (e.g., level of isotopic enrichment, number of labeled taxa, relative abundance of labeled taxa, community richness, community evenness, and beta-diversity) have on the specificity, sensitivity, and balanced accuracy (defined as the product of specificity and sensitivity) of DNA-SIP analyses. Furthermore, SIPSim can predict analytical accuracy and power as a function of experimental design and community characteristics, and thus should be of great use in the design and interpretation of DNA-SIP experiments.},
doi = {10.3389/fmicb.2018.00570},
url = {https://www.osti.gov/biblio/1510497},
journal = {Frontiers in Microbiology},
issn = {1664-302X},
number = ,
volume = 9,
place = {United States},
year = {Wed Mar 28 00:00:00 EDT 2018},
month = {Wed Mar 28 00:00:00 EDT 2018}
}
Web of Science
Works referenced in this record:
Equilibrium Sedimentation of Macromolecules in Density Gradients
journal, July 1957
- Meselson, M.; Stahl, F. W.; Vinograd, J.
- Proceedings of the National Academy of Sciences, Vol. 43, Issue 7
Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation
journal, June 2015
- Pepe-Ranney, Charles; Koechli, Chantal; Potrafka, Ruth
- The ISME Journal, Vol. 10, Issue 2
Using analytical ultracentrifugation to study compositional variation in vertebrate genomes
journal, August 2003
- Clay, Oliver; Douady, Christophe J.; Carels, Nicolas
- European Biophysics Journal, Vol. 32, Issue 5
DNA buoyant density shifts during 15N-DNA stable isotope probing
journal, September 2007
- Cupples, Alison M.; Shaffer, Elizabeth A.; Chee-Sanford, Joanne C.
- Microbiological Research, Vol. 162, Issue 4, p. 328-334
Intra-genomic variation in G + C content and its implications for DNA stable isotope probing: DNA-SIP and intra-genomic variation in G + C content
journal, October 2014
- Youngblut, Nicholas D.; Buckley, Daniel H.
- Environmental Microbiology Reports, Vol. 6, Issue 6
Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs)
journal, May 2007
- Leigh, Mary Beth; Pellizari, Vivian H.; Uhlík, Ondřej
- The ISME Journal, Vol. 1, Issue 2
MFEprimer: multiple factor evaluation of the specificity of PCR primers
journal, November 2008
- Qu, Wubin; Shen, Zhiyong; Zhao, Dongsheng
- Bioinformatics, Vol. 25, Issue 2
GenBank
journal, November 2009
- Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.
- Nucleic Acids Research, Vol. 38, Issue suppl_1
Sedimentation equilibrium of DNA samples heterogeneous in density
journal, September 1972
- Schmid, Carl W.; Hearst, John E.
- Biopolymers, Vol. 11, Issue 9
DNA isolation from soil samples for cloning in different hosts
collection, January 2004
- Kauffmann, Isabelle Melanie; Schmitt, Jutta; Schmid, Rolf D.
- Universität Stuttgart
Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl
journal, June 1962
- Schildkraut, Carl L.; Marmur, Julius; Doty, Paul
- Journal of Molecular Biology, Vol. 4, Issue 6
Use of Inorganic and Organic Nitrogen by Synechococcus spp. and Diatoms on the West Florida Shelf as Measured Using Stable Isotope Probing
journal, September 2009
- Wawrik, B.; Callaghan, A. V.; Bronk, D. A.
- Applied and Environmental Microbiology, Vol. 75, Issue 21
Stable Isotope Probing with 15N Achieved by Disentangling the Effects of Genome G+C Content and Isotope Enrichment on DNA Density
journal, March 2007
- Buckley, D. H.; Huangyutitham, V.; Hsu, S. -F.
- Applied and Environmental Microbiology, Vol. 73, Issue 10
Differential abundance analysis for microbial marker-gene surveys
journal, September 2013
- Paulson, Joseph N.; Stine, O. Colin; Bravo, Héctor Corrada
- Nature Methods, Vol. 10, Issue 12
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
journal, April 2014
- McMurdie, Paul J.; Holmes, Susan
- PLoS Computational Biology, Vol. 10, Issue 4
Microbial seed banks: the ecological and evolutionary implications of dormancy
journal, January 2011
- Lennon, Jay T.; Jones, Stuart E.
- Nature Reviews Microbiology, Vol. 9, Issue 2
DNA stable-isotope probing
journal, April 2007
- Neufeld, Josh D.; Vohra, Jyotsna; Dumont, Marc G.
- Nature Protocols, Vol. 2, Issue 4
Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients: Quantitative analysis of SIP gradients
journal, December 2003
- Lueders, Tillmann; Manefield, Mike; Friedrich, Michael W.
- Environmental Microbiology, Vol. 6, Issue 1
DNA-based stable isotope probing: a link between community structure and function
journal, June 2009
- Uhlík, Ondrej; Jecná, Katerina; Leigh, Mary Beth
- Science of The Total Environment, Vol. 407, Issue 12, p. 3611-3619
Importance of DNA quality in comparative soil microbial community structure analyses
journal, June 2008
- Thakuria, Dwipendra; Schmidt, Olaf; Mac Siúrtáin, Máirtín
- Soil Biology and Biochemistry, Vol. 40, Issue 6
Density-Gradient centrifugation of DNA in a fixed-angle rotor
journal, November 1966
- Flamm, W. G.; Bond, H. E.; Burr, H. E.
- Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis, Vol. 129, Issue 2
DNA isolation from soil samples for cloning in different hosts
journal, June 2004
- Kauffmann, I. M.; Schmitt, J.; Schmid, R. D.
- Applied Microbiology and Biotechnology, Vol. 64, Issue 5
Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture
journal, March 2021
- Rajewski, Alex; Carter-House, Derreck; Stajich, Jason
- BMC Genomics, Vol. 22, Issue 1
Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil
journal, May 2016
- Pepe-Ranney, Charles; Campbell, Ashley N.; Koechli, Chantal N.
- Frontiers in Microbiology, Vol. 7
Quantitative Microbial Ecology through Stable Isotope Probing
journal, August 2015
- Hungate, Bruce A.; Mau, Rebecca L.; Schwartz, Egbert
- Applied and Environmental Microbiology, Vol. 81, Issue 21
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
Waste Not, Want Not: Why Rarefying Microbiome Data is Inadmissible
text, January 2013
- McMurdie, Paul J.; Holmes, Susan
- arXiv
Sedimentation equilibrium of DNA samples heterogeneous in density
journal, September 1972
- Schmid, Carl W.; Hearst, John E.
- Biopolymers, Vol. 11, Issue 9
Density gradient centrifugation in angle-head rotors
journal, December 1964
- Fisher, W. D.; Cline, G. B.; Anderson, N. G.
- Analytical Biochemistry, Vol. 9, Issue 4
DNA buoyant density shifts during 15N-DNA stable isotope probing
journal, September 2007
- Cupples, Alison M.; Shaffer, Elizabeth A.; Chee-Sanford, Joanne C.
- Microbiological Research, Vol. 162, Issue 4, p. 328-334
Importance of DNA quality in comparative soil microbial community structure analyses
journal, June 2008
- Thakuria, Dwipendra; Schmidt, Olaf; Mac Siúrtáin, Máirtín
- Soil Biology and Biochemistry, Vol. 40, Issue 6
Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs)
journal, May 2007
- Leigh, Mary Beth; Pellizari, Vivian H.; Uhlík, Ondřej
- The ISME Journal, Vol. 1, Issue 2
Differential abundance analysis for microbial marker-gene surveys
journal, September 2013
- Paulson, Joseph N.; Stine, O. Colin; Bravo, Héctor Corrada
- Nature Methods, Vol. 10, Issue 12
Niche partitioning of the ubiquitous and ecologically relevant NS5 marine group
journal, February 2022
- Priest, Taylor; Heins, Anneke; Harder, Jens
- The ISME Journal, Vol. 16, Issue 6
Equilibrium Sedimentation of Macromolecules in Density Gradients
journal, July 1957
- Meselson, M.; Stahl, F. W.; Vinograd, J.
- Proceedings of the National Academy of Sciences, Vol. 43, Issue 7
MFEprimer: multiple factor evaluation of the specificity of PCR primers
journal, November 2008
- Qu, Wubin; Shen, Zhiyong; Zhao, Dongsheng
- Bioinformatics, Vol. 25, Issue 2
GenBank
journal, November 2009
- Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.
- Nucleic Acids Research, Vol. 38, Issue suppl_1
Intra-genomic variation in G + C content and its implications for DNA stable isotope probing: DNA-SIP and intra-genomic variation in G + C content
journal, October 2014
- Youngblut, Nicholas D.; Buckley, Daniel H.
- Environmental Microbiology Reports, Vol. 6, Issue 6
High-Sensitivity Stable-Isotope Probing by a Quantitative Terminal Restriction Fragment Length Polymorphism Protocol
journal, October 2011
- Andeer, Peter; Strand, Stuart E.; Stahl, David A.
- Applied and Environmental Microbiology, Vol. 78, Issue 1
Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR.
journal, January 1996
- Suzuki, M. T.; Giovannoni, S. J.
- Applied and environmental microbiology, Vol. 62, Issue 2
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
Comparative Study of Methods for Extraction and Purification of Environmental DNA From Soil and Sludge Samples
journal, January 2006
- Roh, Changhyun; Villatte, Francois; Kim, Byung-Gee
- Applied Biochemistry and Biotechnology, Vol. 134, Issue 2
DNA isolation from soil samples for cloning in different hosts
collection, January 2004
- Kauffmann, Isabelle Melanie; Schmitt, Jutta; Schmid, Rolf D.
- Universität Stuttgart
Waste Not, Want Not: Why Rarefying Microbiome Data is Inadmissible
text, January 2013
- McMurdie, Paul J.; Holmes, Susan
- arXiv
Works referencing / citing this record:
Simulating metagenomic stable isotope probing datasets with MetaSIPSim
journal, January 2020
- Barnett, Samuel E.; Buckley, Daniel H.
- BMC Bioinformatics, Vol. 21, Issue 1
Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment
journal, January 2020
- Kapili, Bennett J.; Barnett, Samuel E.; Buckley, Daniel H.
- The ISME Journal, Vol. 14, Issue 4
Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil
journal, March 2019
- Thomas, François; Corre, Erwan; Cébron, Aurélie
- The ISME Journal, Vol. 13, Issue 7
MFEprimer-3.0: quality control for PCR primers
journal, May 2019
- Wang, Kun; Li, Haiwei; Xu, Yue
- Nucleic Acids Research, Vol. 47, Issue W1
Divergent microbial communities in groundwater and overlying soils exhibit functional redundancy for plant-polysaccharide degradation
journal, March 2019
- Taubert, Martin; Stähly, Jan; Kolb, Steffen
- PLOS ONE, Vol. 14, Issue 3
Ancylomarina psychrotolerans sp. nov., isolated from sediments of Fildes Peninsula and emended the description of genus Ancylomarina
journal, February 2018
- Jia, Chao; Cui, Hong-chang; Han, Yan-qiong
- Antonie van Leeuwenhoek, Vol. 111, Issue 7
MFEprimer-3.0: quality control for PCR primers
journal, May 2019
- Wang, Kun; Li, Haiwei; Xu, Yue
- Nucleic Acids Research, Vol. 47, Issue W1
Simulating metagenomic stable isotope probing datasets with MetaSIPSim
journal, January 2020
- Barnett, Samuel E.; Buckley, Daniel H.
- BMC Bioinformatics, Vol. 21, Issue 1