Impact of catabolic plasmids on host cell physiology

► Interaction between plasmid and host determines their fates in the environment. ► Impact of plasmid carriage to host transcriptome can be comprehensively analyzed. ► Disturbance of host-cell physiology by plasmid carriage leads to metabolic burden. ► Imbalance of metabolic pathways affects the fate of plasmid in the environment. ► Nucleoid-associated proteins are the key determinants for plasmid behavior.