Plasmidomics: studying plasmids as ecological entities beyond their hosts

Bradd Mendoza-Guido, Keilor Rojas-Jimenez

Plasmids are autonomous mobile genetic elements whose ecology extends beyond individual bacterial hosts. As molecular symbionts, they traverse strains, species, and environments, disseminating adaptive genes and shaping microbial community structure through dynamics that are often decoupled from host taxonomy. Plasmidomics—the omics discipline dedicated to the study of plasmids—has revealed that plasmid diversity and distribution respond to environmental gradients independently of their hosts, underscoring their roles as ecological entities. However, the field faces critical methodological constraints: short-read assemblies fragment plasmid sequences, culture-dependent approaches underrepresent environmental diversity, and most metagenomic methods fail to capture plasmid–host associations. In addition, a universally accepted classification framework is still lacking. Advancing plasmidomics will require the integration of long-read sequencing, Hi-C proximity ligation, and ecology-informed classification frameworks grounded in genomic and functional criteria. Together, these approaches are essential to uncover the true diversity, evolutionary significance, and ecological dynamics of plasmids across complex microbial ecosystems.