Open Access

Genome Biology

, volume 23 , issue 1 , publication number 74

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

Lucas R Van Dijk ^{1, 2}

Bruce J Walker ^{1, 3}

Timothy J Straub ^{1, 4}

Colin J Worby ¹

Alexandra Grote ¹

Henry L. Schreiber ^{5, 6}

Christine Anyansi ²

Amy J. Pickering ^{7, 8}

Scott J. Hultgren ^{5, 6}

Abigail L. Manson ¹

Thomas Abeel ^{1, 2}

Ashlee Earl ¹

Hide authors affiliations Show authors affiliations: 8 affiliations

Infectious Disease & Microbiome Program, Broad Institute, Cambridge, USA |

Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands |

Applied Invention, Cambridge, USA |

⁴

Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA |

⁵

Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, USA |

⁶

Center for Women’s Infectious Disease Research (CWIDR), Washington University School of Medicine, St. Louis, USA |

⁷

Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, USA |

⁸

Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, USA |

Publication type: Journal Article

Publication date: 2022-03-07

Springer Nature

Genome Biology

scimago Q1

wos Q1

SJR: 5.710

CiteScore: 17.5

Impact factor: 9.4

ISSN: 14747596, 14656906, 1474760X

DOI: 10.1186/s13059-022-02630-0

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PubMed ID: 35255937

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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Cite this

GOST |

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GOST Copy

Van Dijk L. R. et al. StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities // Genome Biology. 2022. Vol. 23. No. 1. 74

GOST all authors (up to 50) Copy

Van Dijk L. R., Walker B. J., Straub T. J., Worby C. J., Grote A., Schreiber H. L., Anyansi C., Pickering A. J., Hultgren S. J., Manson A. L., Abeel T., Earl A. StrainGE: a toolkit to track and characterize low-abundance strains in complex microbial communities // Genome Biology. 2022. Vol. 23. No. 1. 74

RIS |

Cite this

RIS Copy

TY - JOUR

DO - 10.1186/s13059-022-02630-0

UR - https://doi.org/10.1186/s13059-022-02630-0

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

T2 - Genome Biology

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

PY - 2022

DA - 2022/03/07

PB - Springer Nature

IS - 1

VL - 23

PMID - 35255937

SN - 1474-7596

SN - 1465-6906

SN - 1474-760X

ER -

BibTex

Cite this

BibTex (up to 50 authors) Copy

@article{2022_Van Dijk,

author = {Lucas R Van Dijk and Bruce J Walker and Timothy J Straub and Colin J Worby and Alexandra Grote and Henry L. Schreiber and Christine Anyansi and Amy J. Pickering and Scott J. Hultgren and Abigail L. Manson and Thomas Abeel and Ashlee Earl},

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

journal = {Genome Biology},

year = {2022},

volume = {23},

publisher = {Springer Nature},

month = {mar},

url = {https://doi.org/10.1186/s13059-022-02630-0},

number = {1},

pages = {74},

doi = {10.1186/s13059-022-02630-0}

}

Publisher

Springer Nature

Journal

Genome Biology

scimago Q1

wos Q1

SJR

5.710

CiteScore

17.5

Impact factor

9.4

ISSN

14747596 (Print)

14656906 (Print)

1474760X (Electronic)