StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities

Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genom...

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Autores principales: van Dijk, Lucas R., Walker, Bruce J., Straub, Timothy J., Worby, Colin J., Grote, Alexandra, Schreiber, Henry L., Anyansi, Christine, Pickering, Amy J., Hultgren, Scott J., Manson, Abigail L., Abeel, Thomas, Earl, Ashlee M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8900328/
https://www.ncbi.nlm.nih.gov/pubmed/35255937
http://dx.doi.org/10.1186/s13059-022-02630-0
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author van Dijk, Lucas R.
Walker, Bruce J.
Straub, Timothy J.
Worby, Colin J.
Grote, Alexandra
Schreiber, Henry L.
Anyansi, Christine
Pickering, Amy J.
Hultgren, Scott J.
Manson, Abigail L.
Abeel, Thomas
Earl, Ashlee M.
author_facet van Dijk, Lucas R.
Walker, Bruce J.
Straub, Timothy J.
Worby, Colin J.
Grote, Alexandra
Schreiber, Henry L.
Anyansi, Christine
Pickering, Amy J.
Hultgren, Scott J.
Manson, Abigail L.
Abeel, Thomas
Earl, Ashlee M.
author_sort van Dijk, Lucas R.
collection PubMed
description Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which deconvolves strain mixtures and characterizes component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools. StrainGE is able to identify strains at 0.1x coverage and detect variants for multiple conspecific strains within a sample from coverages as low as 0.5x. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02630-0.
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spelling pubmed-89003282022-03-17 StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities van Dijk, Lucas R. Walker, Bruce J. Straub, Timothy J. Worby, Colin J. Grote, Alexandra Schreiber, Henry L. Anyansi, Christine Pickering, Amy J. Hultgren, Scott J. Manson, Abigail L. Abeel, Thomas Earl, Ashlee M. Genome Biol Method Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which deconvolves strain mixtures and characterizes component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools. StrainGE is able to identify strains at 0.1x coverage and detect variants for multiple conspecific strains within a sample from coverages as low as 0.5x. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02630-0. BioMed Central 2022-03-07 /pmc/articles/PMC8900328/ /pubmed/35255937 http://dx.doi.org/10.1186/s13059-022-02630-0 Text en © The Author(s) 2022 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
van Dijk, Lucas R.
Walker, Bruce J.
Straub, Timothy J.
Worby, Colin J.
Grote, Alexandra
Schreiber, Henry L.
Anyansi, Christine
Pickering, Amy J.
Hultgren, Scott J.
Manson, Abigail L.
Abeel, Thomas
Earl, Ashlee M.
StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities
title StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities
title_full StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities
title_fullStr StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities
title_full_unstemmed StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities
title_short StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities
title_sort strainge: a toolkit to track and characterize low-abundance strains in complex microbial communities
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8900328/
https://www.ncbi.nlm.nih.gov/pubmed/35255937
http://dx.doi.org/10.1186/s13059-022-02630-0
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