Citrobacter rodentium, which colonizes the gut mucosa via formation of attaching and effacing (A/E) lesions, causes transmissible colonic hyperplasia. The aim of this study was to evaluate if prophylactic treatment with Bifidobacterium breve UCC2003 can improve the outcome of C. rodentium infection. Six week old Albino C57BL/6 mice were pre-treated for 3 days with B. breve, challenged with bioluminescent C. rodentium and administered B. breve or PBS-C for 8 days post infection; control mice were either administered B. breve and mock infected with PBS, or were mock treated with PBS-C and mock infected with PBS. C. rodentium colonisation was monitored by bacterial enumeration from faeces and by a combination of both 2D bioluminescence imaging (BLI) and composite 3D diffuse light imaging tomography with microCT imaging (DLIT-microCT). At day 8 post infection, colons were removed and assessed for crypt hyperplasia, histology by light microscopy, bacterial colonisation by immunofluorescence, and A/E lesion formation by electron microscopy. Prophylactic administration of B. breve did not prevent C. rodentium colonisation or A/E lesion formation. However, this treatment did alter C. rodentium distribution within the large intestine and significantly reduced colonic crypt hyperplasia at the peak of bacterial infection. These results show that B. breve could not competitively exclude C. rodentium, but reduced pathogen-induced colonic inflammation.