SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments
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....
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-03-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/article/10.3389/fmicb.2018.00570/full |
| _version_ | 1818497835425857536 |
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| author | Nicholas D. Youngblut Samuel E. Barnett Daniel H. Buckley |
| author_facet | Nicholas D. Youngblut Samuel E. Barnett Daniel H. Buckley |
| author_sort | Nicholas D. Youngblut |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-10T18:50:21Z |
| format | Article |
| id | doaj.art-e4dcefd9093f40b2bd8cd1470aeab813 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-10T18:50:21Z |
| publishDate | 2018-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-e4dcefd9093f40b2bd8cd1470aeab8132022-12-22T01:37:21ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-03-01910.3389/fmicb.2018.00570309232SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP ExperimentsNicholas D. YoungblutSamuel E. BarnettDaniel H. BuckleyDNA 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.http://journal.frontiersin.org/article/10.3389/fmicb.2018.00570/fullDNA-SIPSIPmethodmicrobialcommunityfunction |
| spellingShingle | Nicholas D. Youngblut Samuel E. Barnett Daniel H. Buckley SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments Frontiers in Microbiology DNA-SIP SIP method microbial community function |
| title | SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments |
| title_full | SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments |
| title_fullStr | SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments |
| title_full_unstemmed | SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments |
| title_short | SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments |
| title_sort | sipsim a modeling toolkit to predict accuracy and aid design of dna sip experiments |
| topic | DNA-SIP SIP method microbial community function |
| url | http://journal.frontiersin.org/article/10.3389/fmicb.2018.00570/full |
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