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SIPSim：一种用于预测DNA-SIP实验准确性并辅助其设计的建模工具包。

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments.

作者信息

Youngblut Nicholas D, Barnett Samuel E, Buckley Daniel H

机构信息

School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.

出版信息

Front Microbiol. 2018 Mar 28;9:570. doi: 10.3389/fmicb.2018.00570. eCollection 2018.

DOI:10.3389/fmicb.2018.00570
PMID:29643843
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5882788/
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 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.

摘要

DNA 稳定同位素探测（DNA-SIP）是一种强大的方法，可将微生物群落中的身份与功能联系起来。DNA-SIP 与多重高通量 DNA 测序相结合，能够同时绘制数千个微生物分类单元的同化动态图谱。因此，高通量测序辅助的 SIP 具有巨大潜力，可揭示微生物食物网中的碳氮交换模式。分析 DNA-SIP 数据有几种不同方法，尽管 SIP 实验功能强大，但在广泛的实验参数范围内全面评估方法准确性仍然困难。我们开发了一个模拟 DNA-SIP 数据的工具集（SIPSim），并使用该工具集系统地评估分析 DNA-SIP 数据的不同方法。具体而言，我们利用 SIPSim 评估关键实验参数（如同位素富集水平、标记分类单元数量、标记分类单元的相对丰度、群落丰富度、群落均匀度和β-多样性）对 DNA-SIP 分析的特异性、敏感性和平衡准确性（定义为特异性与敏感性的乘积）的影响。此外，SIPSim 可以根据实验设计和群落特征预测分析准确性和效能，因此在 DNA-SIP 实验的设计和解读中应具有很大用途。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8825/5882788/30049dca0ddf/fmicb-09-00570-g0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8825/5882788/baabc7d7e5b2/fmicb-09-00570-g0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8825/5882788/5eb3f5c0c3c8/fmicb-09-00570-g0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8825/5882788/a269e95da86b/fmicb-09-00570-g0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8825/5882788/b526bbf25787/fmicb-09-00570-g0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8825/5882788/da9a016ceefe/fmicb-09-00570-g0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8825/5882788/30049dca0ddf/fmicb-09-00570-g0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8825/5882788/baabc7d7e5b2/fmicb-09-00570-g0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8825/5882788/5eb3f5c0c3c8/fmicb-09-00570-g0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8825/5882788/a269e95da86b/fmicb-09-00570-g0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8825/5882788/b526bbf25787/fmicb-09-00570-g0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8825/5882788/da9a016ceefe/fmicb-09-00570-g0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8825/5882788/30049dca0ddf/fmicb-09-00570-g0008.jpg

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