“…Taken together, our data extend previous work, 10,11,37,39,42,44,45,47,49,50,76 highlight that in vivo studies of host-pathogen interactions are highly sensitive to the experimental conditions, and may be subject to confounding effects that limit reproducibility. The general approach presented here-a combination of littermate controlled infections, host cell typespecific gene knockouts, genetically tagged bacterial consortia, mathematical modeling and high-resolution imaging of the infected cells/organs-allowed us to decipher the impact of specific host responses in vivo.…”