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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Detalles Bibliográficos
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
Descripción
Sumario: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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