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

Lucas R. van Dijk; Bruce J. Walker; Timothy J. Straub; Colin J. Worby; Alexandra Grote; Henry L. Schreiber; Christine Anyansi; Amy J. Pickering; Scott J. Hultgren; Abigail L. Manson; Thomas Abeel; Ashlee M. Earl

doi:10.1186/s13059-022-02630-0

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

Lucas R. van Dijk, Bruce J. Walker, Timothy J. Straub, Colin J. Worby, Alexandra Grote, Henry L. Schreiber, Christine Anyansi, Amy J. Pickering, Scott J. Hultgren, Abigail L. Manson, Thomas Abeel, Ashlee M. Earl^*

^*Corresponding author for this work

Pattern Recognition and Bioinformatics

Research output: Contribution to journal › Article › Scientific › peer-review

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Abstract

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.

Original language	English
Article number	74
Number of pages	27
Journal	Genome biology
Volume	23
Issue number	1
DOIs	https://doi.org/10.1186/s13059-022-02630-0
Publication status	Published - 2022

Keywords

Metagenomics
Microbiome
Strain-tracking

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10.1186/s13059-022-02630-0

s13059-022-02630-0Final published version, 4.14 MBLicence: CC BY

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

abstract = "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.",

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T2 - a toolkit to track and characterize low-abundance strains in complex microbial communities

AU - van Dijk, Lucas R.

AU - Walker, Bruce J.

AU - Straub, Timothy J.

AU - Worby, Colin J.

AU - Grote, Alexandra

AU - Schreiber, Henry L.

AU - Anyansi, Christine

AU - Pickering, Amy J.

AU - Hultgren, Scott J.

AU - Manson, Abigail L.

AU - Abeel, Thomas

AU - Earl, Ashlee M.

PY - 2022

Y1 - 2022

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AB - 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.

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KW - Strain-tracking

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

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Keywords

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