Huson, DH, Steel, M, El-Hadidi, M et al. (3 more authors) (2017) A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples. Journal of Biotechnology, 250. pp. 45-50. ISSN 0168-1656
Abstract
One important question in microbiome analysis is how to assess the homogeneity of the microbial composition in a given environment, with respect to a given analysis method. Do different microbial samples taken from the same environment follow the same taxonomic distribution of organisms, or the same distribution of functions? Here we provide a non-parametric statistical “triangulation test” to address this type of question. The test requires that multiple replicates are available for each of the biological samples, and it is based on three-way computational comparisons of samples. To illustrate the application of the test, we collected three biological samples taken from different locations in one piece of human stool, each represented by three replicates, and analyzed them using MEGAN. (Despite its name, the triangulation test does not require that the number of biological samples or replicates be three.) The triangulation test rejects the null hypothesis that the three biological samples exhibit the same distribution of taxa or function (error probability ≤0.05), indicating that the microbial composition of the investigated human stool is not homogenous on a macroscopic scale, suggesting that pooling material from multiple locations is a reasonable practice. We provide an implementation of the test in our open source program MEGAN Community Edition.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2016 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/) |
Keywords: | Metagenomics; Taxonomic composition; Functional diversity; Environmental inhomogeneity; Statistical testing |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Medicine and Health (Leeds) > Institute of Molecular Medicine (LIMM) (Leeds) > Section of Molecular Gastroenterology (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 11 Apr 2017 15:42 |
Last Modified: | 08 Sep 2017 13:01 |
Published Version: | https://doi.org/10.1016/j.jbiotec.2016.10.020 |
Status: | Published |
Publisher: | Elsevier |
Identification Number: | 10.1016/j.jbiotec.2016.10.020 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:114961 |