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Plasmidomics \u2013 the omics discipline dedicated to the study of plasmids \u2013 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\u2013host 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, meta-epigenomics and ecology-informed classification frameworks grounded in genomic and functional criteria. 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