Multiomic analysis of the compensatory evolution of pB1000 in Haemophilus influenzae RdKW20

This work combines experimental evolution with an integrative multiomic analysis aiming to comprehend the plasmid/host co-adaptation process. We designed a five replicate experimental evolution assay in which we obtained: (1) Rd-T0: non-evolved plasmid-free H. influenzae populations; (2) Rd/pB-T0: populations that had recently acquired the plasmid pB1000; and (3) Rd/pB-T100: populations that had evolved with pB1000 and compensated its fitness cost. Additionally, we include in our study plasmid-free populations evolved for the same generations but without the plasmid (Rd-T100). Once we had all the populations, we analyzed the genomic, transcriptomic and metabolomic modifications identified in the evolved pB1000-bearing bacteria responsible for the plasmid compensation.