Comparison of assembly methods for Long-read sequencing of plasmid communities

Advisor:
Nicole Ricker (Pathobiology)

The role of plasmids in facilitating bacterial evolution is well-established, yet studies investigating the population dynamics of plasmids within different ecosystems are scarce. Animal agriculture is an important reservoir for the evolution and dissemination of plasmids that carry antimicrobial resistance (AMR) genes. Recently, we isolated bacterial plasmid communities from fecal samples of swine, sequenced these communities using the Oxford nanopore MINion sequencer and assembled a small number of intact plasmids carrying AMR genes. Although this was consistent with the goals of this project, the diversity of plasmid replicons identified in the samples indicates that only a very small fraction of the total plasmid community was successfully assembled. As metagenomic assemblers are not specifically designed for this type of data, this project therefore aims to evaluate available software programs for metagenomic assembly and determine their suitability for assembling mixed plasmid communities. The project will involve researching suitable tools and running a comparison of the current software available, as well as investigating the biological causes of failed assemblies.