SNV-FEAST: microbial source tracking with single nucleotide variants

Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleotide variants (SNVs) may be more informative because of their...

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Detalles Bibliográficos
Autores principales: Briscoe, Leah, Halperin, Eran, Garud, Nandita R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10150486/
https://www.ncbi.nlm.nih.gov/pubmed/37121994
http://dx.doi.org/10.1186/s13059-023-02927-8
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author Briscoe, Leah
Halperin, Eran
Garud, Nandita R.
author_facet Briscoe, Leah
Halperin, Eran
Garud, Nandita R.
author_sort Briscoe, Leah
collection PubMed
description Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleotide variants (SNVs) may be more informative because of their high specificity to certain sources. To overcome the computational burden of utilizing all SNVs for a given sample, we introduce a novel method to identify signature SNVs for source tracking. Signature SNVs used as input into a previously designed source tracking algorithm, FEAST, can more accurately estimate contributions than species and provide novel insights, demonstrated in three case studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02927-8.
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spelling pubmed-101504862023-05-02 SNV-FEAST: microbial source tracking with single nucleotide variants Briscoe, Leah Halperin, Eran Garud, Nandita R. Genome Biol Method Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleotide variants (SNVs) may be more informative because of their high specificity to certain sources. To overcome the computational burden of utilizing all SNVs for a given sample, we introduce a novel method to identify signature SNVs for source tracking. Signature SNVs used as input into a previously designed source tracking algorithm, FEAST, can more accurately estimate contributions than species and provide novel insights, demonstrated in three case studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02927-8. BioMed Central 2023-04-30 /pmc/articles/PMC10150486/ /pubmed/37121994 http://dx.doi.org/10.1186/s13059-023-02927-8 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Briscoe, Leah
Halperin, Eran
Garud, Nandita R.
SNV-FEAST: microbial source tracking with single nucleotide variants
title SNV-FEAST: microbial source tracking with single nucleotide variants
title_full SNV-FEAST: microbial source tracking with single nucleotide variants
title_fullStr SNV-FEAST: microbial source tracking with single nucleotide variants
title_full_unstemmed SNV-FEAST: microbial source tracking with single nucleotide variants
title_short SNV-FEAST: microbial source tracking with single nucleotide variants
title_sort snv-feast: microbial source tracking with single nucleotide variants
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10150486/
https://www.ncbi.nlm.nih.gov/pubmed/37121994
http://dx.doi.org/10.1186/s13059-023-02927-8
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