Shiga toxin 2 (Stx2)-converting bacteriophages can infect and lysogenize other bacteria in vivo and in vitro, and, thus, contribute to a genotypic heterogeneity of infected host. However, the global transcription patterns accompanying the lysogenic infection of E. coli host have not been clearly resolved. In this study, gene expression profiles of Stx2 phage ФMin27(Δstx::cat) converted and native E. coli MG1655 hosts were compared using microarray assay. The ФMin27(Δstx::cat) conversion had a direct effect on the global expression of bacterial host genes as 166 genes were found to be differentially expressed (104 up-regulated and 62 down-regulated). These genes were predominantly responsible for bacterial central metabolism, transport and transcription. It was shown that in addition to the down-regulation of genes involved in synthesis of thiamine and protein transporters, expression of genes associated with bacterial energy production (e.g., fadABDEHIJL, aceK, and acnA) was also suppressed. Conversely, most up-regulated genes were transport genes, flagellar synthesis genes (fliDESTZ), and acid resistance genes (e.g., gadEW, hdeABD, and adiY). Futhermore, conversion of ФMin27(Δstx::cat) was shown to change physiological properties of the host cell. In comparison with the uninfected cells the converted bacteria host had increased acid tolerance and promoted swimming motility on a semisolid agar surface.