plasmidome

A plasmidome is the complete set of plasmids found within a given microbiological sample or environment. Plasmids are extrachromosomal, circular DNA elements that replicate independently from the host chromosome and often carry genes that confer advantageous traits. The plasmidome is conceptually analogous to the metagenome and the pangenome, but focuses on plasmids and their mobile gene content rather than chromosomal genes.

Plasmids vary in size, copy number, host range, and mobility. They commonly harbor replication initiation genes, maintenance systems, and mobility genes such as tra and mob. The cargo of plasmids includes antibiotic resistance genes, metal resistance, virulence factors, catabolic enzymes, and other traits that influence host fitness or ecology. The plasmidome reflects both lineage-associated plasmids and those transferred across species.

Studying plasmidomes involves isolation or enrichment of plasmid DNA, followed by sequencing and computational analysis. Short- and long-read sequencing are used, with approaches like plasmidome sequencing or total metagenome sequencing with plasmid reconstruction. Tools such as MOB-suite, PlasmidFinder, and plasmidSPAdes assist in identifying plasmids and predicting their mobility and host range. Challenges include assembly of repetitive plasmid regions, multi-copy plasmids, and distinguishing plasmids from integrated elements.

Applications of plasmidome analysis include monitoring horizontal gene transfer, tracking the spread of antibiotic resistance, and understanding microbial community ecology. In clinical and environmental settings, plasmidome data can inform risk assessment and intervention strategies. Limitations include sampling bias, incomplete plasmid recovery, and uncertainty about the original host of plasmids in environmental samples.