Strain profiling and epidemiology of bacterial species from metagenomic sequencing.

ABSTRACT: Microbial communities are often composed by complex mixtures of multiple strains of the same species, characterized by a wide genomic and phenotypic variability. Computational methods able to identify, quantify and classify the different strains present in a sample are essential to fully exploit the potential of metagenomic sequencing in microbial ecology, with applications that range from the epidemiology of infectious diseases to the characterization of the dynamics of microbial colonization. Here we present a computational approach that uses the available genomic data to reconstruct complex strain profiles from metagenomic sequencing, quantifying the abundances of the different strains and cataloging them according to the population structure of the species. We validate the method on sy

SUBMITTER: Albanese D 

PROVIDER: S-EPMC5741664 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature