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- Benjamin J Ridenhour
- Department of Biological Sciences, University of Idaho , Moscow, ID, USA
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- Sarah L Brooker
- Bioinformatics and Computational Biology Program, University of Idaho , Moscow, ID, USA
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- Janet E Williams
- Bioinformatics and Computational Biology Program, University of Idaho , Moscow, ID, USA
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- James T Van Leuven
- Center for Modeling Complex Interactions, University of Idaho , Moscow, ID, USA
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- Aaron W Miller
- Department of Biology, University of Utah , Salt Lake City, UT, USA
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- M Denise Dearing
- Department of Biology, University of Utah , Salt Lake City, UT, USA
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- Christopher H Remien
- Bioinformatics and Computational Biology Program, University of Idaho , Moscow, ID, USA
書誌事項
- 公開日
- 2017-08-08
- 権利情報
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- https://academic.oup.com/pages/standard-publication-reuse-rights
- http://www.springer.com/tdm
- DOI
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- 10.1038/ismej.2017.107
- 公開者
- Oxford University Press (OUP)
この論文をさがす
説明
<jats:title>Abstract</jats:title> <jats:p>As sequencing technologies have advanced, the amount of information regarding the composition of bacterial communities from various environments (for example, skin or soil) has grown exponentially. To date, most work has focused on cataloging taxa present in samples and determining whether the distribution of taxa shifts with exogenous covariates. However, important questions regarding how taxa interact with each other and their environment remain open thus preventing in-depth ecological understanding of microbiomes. Time-series data from 16S rDNA amplicon sequencing are becoming more common within microbial ecology, but methods to infer ecological interactions from these longitudinal data are limited. We address this gap by presenting a method of analysis using Poisson regression fit with an elastic-net penalty that (1) takes advantage of the fact that the data are time series; (2) constrains estimates to allow for the possibility of many more interactions than data; and (3) is scalable enough to handle data consisting of thousands of taxa. We test the method on gut microbiome data from white-throated woodrats (Neotoma albigula) that were fed varying amounts of the plant secondary compound oxalate over a period of 22 days to estimate interactions between OTUs and their environment.</jats:p>
収録刊行物
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- The ISME Journal
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The ISME Journal 11 (11), 2526-2537, 2017-08-08
Oxford University Press (OUP)
