Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands.

ABSTRACT: Metagenomic methods enable the simultaneous characterization of microbial communities without time-consuming and bias-inducing culturing. Metagenome-assembled genome (MAG) binning methods aim to reassemble individual genomes from this data. However, the recovery of mobile genetic elements (MGEs), such as plasmids and genomic islands (GIs), by binning has not been well characterized. Given the association of antimicrobial resistance (AMR) genes and virulence factor (VF) genes with MGEs, studying their transmission is a public-health priority. The variable copy number and sequence composition of MGEs makes them potentially problematic for MAG binning methods. To systematically investigate this issue, we simulated a low-complexity metagenome comprising 30 GI-rich and plasmid-containing bacter

SUBMITTER: Maguire F 

PROVIDER: S-EPMC7660262 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature