Host adaptation of an attenuated live vaccine in a mouse model

In Hapfelmeier lab, they have developed an attenuated live vaccine making Salmonella Thyphimurium auxotrophic for peptidoglycan constituants. In order to test the safety of the live vaccine, they performed a long term experiment in a mouse model for at least 4 years. I am studying the evolution of the auxotrophic Salmonella : how the bacttrium evolved genetically but also phenotypically. I am willing to also understand how the immune system and the microbiota have contributed to the evolution of Salmonella. For that, I would like to study the transcriptome and proteome of both the bacterium and the host.