Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L(2)UniFrac
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 variabilit...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Cold Spring Harbor Laboratory
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9915697/ https://www.ncbi.nlm.nih.gov/pubmed/36778267 http://dx.doi.org/10.1101/2023.02.02.526854 |
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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 | 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 achieved 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. 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. A prototype implementation is provided at: https://github.com/KoslickiLab/L2-UniFrac.git. |
format | Online Article Text |
id | pubmed-9915697 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Cold Spring Harbor Laboratory |
record_format | MEDLINE/PubMed |
spelling | pubmed-99156972023-02-11 Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L(2)UniFrac Wei, Wei Millward, Andrew Koslicki, David bioRxiv Article 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 achieved 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. 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. A prototype implementation is provided at: https://github.com/KoslickiLab/L2-UniFrac.git. Cold Spring Harbor Laboratory 2023-02-03 /pmc/articles/PMC9915697/ /pubmed/36778267 http://dx.doi.org/10.1101/2023.02.02.526854 Text en https://creativecommons.org/licenses/by-nc/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License (https://creativecommons.org/licenses/by-nc/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator. |
spellingShingle | Article 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 | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9915697/ https://www.ncbi.nlm.nih.gov/pubmed/36778267 http://dx.doi.org/10.1101/2023.02.02.526854 |
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