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Title: 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:
 [1];  [1];  [1]
  1. 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) (SC-23)
OSTI Identifier:
1510497
Grant/Contract Number:  
SC0004486; SC0010558
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. doi:10.3389/fmicb.2018.00570.
Youngblut, Nicholas D., Barnett, Samuel E., and Buckley, Daniel H. Wed . "SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments". United States. doi: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},
journal = {Frontiers in Microbiology},
issn = {1664-302X},
number = ,
volume = 9,
place = {United States},
year = {2018},
month = {3}
}

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Works referenced in this record:

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journal, September 2007

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