InStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains.

ABSTRACT: Coexisting microbial cells of the same species often exhibit genetic variation that can affect phenotypes ranging from nutrient preference to pathogenicity. Here we present inStrain, a program that uses metagenomic paired reads to profile intra-population genetic diversity (microdiversity) across whole genomes and compares microbial populations in a microdiversity-aware manner, greatly increasing the accuracy of genomic comparisons when benchmarked against existing methods. We use inStrain to profile >1,000 fecal metagenomes from newborn premature infants and find that siblings share significantly more strains than unrelated infants, although identical twins share no more strains than fraternal siblings. Infants born by cesarean section harbor Klebsiella with significantly higher nucleotid

SUBMITTER: Olm MR 

PROVIDER: S-EPMC9223867 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature