Bordetella pertussis, the causative agent of whooping cough, infects and sickens millions around the world every year, both in wealthy and resource-constrained regions. In order to protect human populations, we need to move beyond the current vaccine and treatment methods and gain a greater understanding of how it transmits. Bordetella bronchiseptica, a related pathogen which primarily affects non-human mammals, is used in laboratory settings to study these transmission dynamics. To understand how the immune system functions in controlling transmission, we infected immune-compromised mice with B. bronchiseptica and observed the importance of TLR4-induced innate immunity in controlling colonization, shedding, and transmission, and the correlation of the neutrophil response to higher shedding of infectious particles. We also studied the intracellular survival of B. bronchiseptica in Dictyostelium discoideum, a common soil amoeba, and showed that non-mammalian eukaryotic cells are a potential environmental reservoir. By understanding how B. bronchiseptica transmits through investigation of relevant immune mechanisms and environmental reservoirs, we can move closer to finding ways to interrupting the chain of transmission of B. pertussis in humans.