The type IV secretion system (T4SS) contributes to Brucella intracellular survival through its effector proteins. Comparative proteomic analysis showed that intracellular survival proteins are expressed differentially in a virB mutant. Interestingly, several outer membrane proteins (OMPs) are also differentially expressed, implying that T4SS might affect the OM properties of Brucella. To further evaluate the impact of T4SS on OM, in the present study, the OM proteomes were isolated and compared. Many more products of OMPs, particularly different products of the Omp25/Omp31 family, were found to be altered in the virB mutant. The transcription profiles of Omp25/Omp31 were different from those of their protein products, implying their regulation by virB at both transcriptional and post-transcriptional levels. The virB mutant aggregates at a high cell density and produces exopolysaccharide, a phenotype resembling that of the vjbR mutant. The virB mutant showed increased sensitivity to polymyxin B and decreased survival under oxidative, high-salt and high-osmolarity stresses, indicating drastic membrane alterations. These results indicated that in addition to being an effector protein secretion system, T4SS affects OM properties that might be important for the adaptation of Brucella to both in vitro and in vivo hostile environments.