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Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L(2)UniFrac
MOTIVATION: Metagenomic samples have high spatiotemporal variability. Hence, it is useful to summarize and characterize the microbial makeup of a given environment in a way that is biologically reasonable and interpretable. The UniFrac metric has been a robust and widely used metric for measuring th...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10311324/ https://www.ncbi.nlm.nih.gov/pubmed/37387190 http://dx.doi.org/10.1093/bioinformatics/btad238 |
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author | Wei, Wei Millward, Andrew Koslicki, David |
author_facet | Wei, Wei Millward, Andrew Koslicki, David |
author_sort | Wei, Wei |
collection | PubMed |
description | MOTIVATION: Metagenomic samples have high spatiotemporal variability. Hence, it is useful to summarize and characterize the microbial makeup of a given environment in a way that is biologically reasonable and interpretable. The UniFrac metric has been a robust and widely used metric for measuring the variability between metagenomic samples. We propose that the characterization of metagenomic environments can be improved by finding the average, a.k.a. the barycenter, among the samples with respect to the UniFrac distance. However, it is possible that such a UniFrac-average includes negative entries, making it no longer a valid representation of a metagenomic community. RESULTS: To overcome this intrinsic issue, we propose a special version of the UniFrac metric, termed L(2)UniFrac, which inherits the phylogenetic nature of the traditional UniFrac and with respect to which one can easily compute the average, producing biologically meaningful environment-specific “representative samples.” We demonstrate the usefulness of such representative samples as well as the extended usage of L(2)UniFrac in efficient clustering of metagenomic samples, and provide mathematical characterizations and proofs to the desired properties of L(2)UniFrac. AVAILABILITY AND IMPLEMENTATION: A prototype implementation is provided at https://github.com/KoslickiLab/L2-UniFrac.git. All figures, data, and analysis can be reproduced at https://github.com/KoslickiLab/L2-UniFrac-Paper |
format | Online Article Text |
id | pubmed-10311324 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-103113242023-07-01 Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L(2)UniFrac Wei, Wei Millward, Andrew Koslicki, David Bioinformatics Bioinformatics of Microbes and Microbiomes MOTIVATION: Metagenomic samples have high spatiotemporal variability. Hence, it is useful to summarize and characterize the microbial makeup of a given environment in a way that is biologically reasonable and interpretable. The UniFrac metric has been a robust and widely used metric for measuring the variability between metagenomic samples. We propose that the characterization of metagenomic environments can be improved by finding the average, a.k.a. the barycenter, among the samples with respect to the UniFrac distance. However, it is possible that such a UniFrac-average includes negative entries, making it no longer a valid representation of a metagenomic community. RESULTS: To overcome this intrinsic issue, we propose a special version of the UniFrac metric, termed L(2)UniFrac, which inherits the phylogenetic nature of the traditional UniFrac and with respect to which one can easily compute the average, producing biologically meaningful environment-specific “representative samples.” We demonstrate the usefulness of such representative samples as well as the extended usage of L(2)UniFrac in efficient clustering of metagenomic samples, and provide mathematical characterizations and proofs to the desired properties of L(2)UniFrac. AVAILABILITY AND IMPLEMENTATION: A prototype implementation is provided at https://github.com/KoslickiLab/L2-UniFrac.git. All figures, data, and analysis can be reproduced at https://github.com/KoslickiLab/L2-UniFrac-Paper Oxford University Press 2023-06-30 /pmc/articles/PMC10311324/ /pubmed/37387190 http://dx.doi.org/10.1093/bioinformatics/btad238 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Bioinformatics of Microbes and Microbiomes Wei, Wei Millward, Andrew Koslicki, David Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L(2)UniFrac |
title | Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L(2)UniFrac |
title_full | Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L(2)UniFrac |
title_fullStr | Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L(2)UniFrac |
title_full_unstemmed | Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L(2)UniFrac |
title_short | Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L(2)UniFrac |
title_sort | finding phylogeny-aware and biologically meaningful averages of metagenomic samples: l(2)unifrac |
topic | Bioinformatics of Microbes and Microbiomes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10311324/ https://www.ncbi.nlm.nih.gov/pubmed/37387190 http://dx.doi.org/10.1093/bioinformatics/btad238 |
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