Work

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

Year: 2022

Type: article

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.

Source: Genome biology

DOI: 10.1186/s13059-022-02630-0

Authors: 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

Institutions: Broad Institute, Delft University of Technology, Harvard University, Washington University in St. Louis, Tufts University, University of California, Berkeley

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $5,030

Funders: U.S. Department of Health and Human Services, National Institutes of Health, National Institute of Allergy and Infectious Diseases, National Institute of Diabetes and Digestive and Kidney Diseases

Awards: Advancing genomic, transcriptomic and functional approaches to combat globally important and emerging pathogens, G1294447136, G2898696312, Human MAIT celis in airway mucosal immune responses to intracellular infections, Epidemiologic and molecular basis of the gut-urinary tract axis in urinary tract infection, G925855612

OpenAlex ID: W4221044588

FWCI: 6.444

Cites: 54

Cited by: 99

Related to: 10