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

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.ORCID

Abstract

AbstractHuman-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.

Funder

National Institute of Allergy and Infectious Diseases

National Institute of Diabetes and Digestive and Kidney Diseases

Publisher

Springer Science and Business Media LLC

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