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

Autor: van Dijk LR; Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA.; Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands., Walker BJ; Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA.; Applied Invention, Cambridge, MA, USA., Straub TJ; Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA.; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA., Worby CJ; Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA., Grote A; Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA., Schreiber HL 4th; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.; Center for Women's Infectious Disease Research (CWIDR), Washington University School of Medicine, St. Louis, MO, 63110, USA., Anyansi C; Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands., Pickering AJ; Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA.; Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA., Hultgren SJ; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.; Center for Women's Infectious Disease Research (CWIDR), Washington University School of Medicine, St. Louis, MO, 63110, USA., Manson AL; Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA., Abeel T; Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA.; Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands., Earl AM; Infectious Disease & Microbiome Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA. aearl@broadinstitute.org.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2022 Mar 07; Vol. 23 (1), pp. 74. Date of Electronic Publication: 2022 Mar 07.
DOI: 10.1186/s13059-022-02630-0
Abstrakt: 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.
(© 2022. The Author(s).)
Databáze: MEDLINE
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