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Statistical evaluation of diet-microbe associations
BACKGROUND: Statistical evaluation of the association between microbial abundance and dietary variables can be done in various ways. Currently, there is no consensus on which methods are to be preferred in which circumstances. Application of particular methods seems to be based on the tradition of a...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6506950/ https://www.ncbi.nlm.nih.gov/pubmed/31072384 http://dx.doi.org/10.1186/s12866-019-1464-0 |
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author | Zhang, Xiang Nieuwdorp, Max Groen, Albert K. Zwinderman, Aeiko H. |
author_facet | Zhang, Xiang Nieuwdorp, Max Groen, Albert K. Zwinderman, Aeiko H. |
author_sort | Zhang, Xiang |
collection | PubMed |
description | BACKGROUND: Statistical evaluation of the association between microbial abundance and dietary variables can be done in various ways. Currently, there is no consensus on which methods are to be preferred in which circumstances. Application of particular methods seems to be based on the tradition of a particular research group, availability of experience with particular software, or depending on the outcomes of the analysis. RESULTS: We applied four popular methods including edgeR, limma, metagenomeSeq and shotgunFunctionalizeR, to evaluate the association between dietary variables and abundance of microbes. We found large difference in results between the methods. Our simulation studies revealed that no single method was optimal. CONCLUSIONS: We advise researchers to run multiple analyses and focus on the significant findings identified by multiple methods in order to achieve a better control of false discovery rate, although the false discovery rate can still be substantial. |
format | Online Article Text |
id | pubmed-6506950 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-65069502019-05-13 Statistical evaluation of diet-microbe associations Zhang, Xiang Nieuwdorp, Max Groen, Albert K. Zwinderman, Aeiko H. BMC Microbiol Research Article BACKGROUND: Statistical evaluation of the association between microbial abundance and dietary variables can be done in various ways. Currently, there is no consensus on which methods are to be preferred in which circumstances. Application of particular methods seems to be based on the tradition of a particular research group, availability of experience with particular software, or depending on the outcomes of the analysis. RESULTS: We applied four popular methods including edgeR, limma, metagenomeSeq and shotgunFunctionalizeR, to evaluate the association between dietary variables and abundance of microbes. We found large difference in results between the methods. Our simulation studies revealed that no single method was optimal. CONCLUSIONS: We advise researchers to run multiple analyses and focus on the significant findings identified by multiple methods in order to achieve a better control of false discovery rate, although the false discovery rate can still be substantial. BioMed Central 2019-05-09 /pmc/articles/PMC6506950/ /pubmed/31072384 http://dx.doi.org/10.1186/s12866-019-1464-0 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Zhang, Xiang Nieuwdorp, Max Groen, Albert K. Zwinderman, Aeiko H. Statistical evaluation of diet-microbe associations |
title | Statistical evaluation of diet-microbe associations |
title_full | Statistical evaluation of diet-microbe associations |
title_fullStr | Statistical evaluation of diet-microbe associations |
title_full_unstemmed | Statistical evaluation of diet-microbe associations |
title_short | Statistical evaluation of diet-microbe associations |
title_sort | statistical evaluation of diet-microbe associations |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6506950/ https://www.ncbi.nlm.nih.gov/pubmed/31072384 http://dx.doi.org/10.1186/s12866-019-1464-0 |
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