Bordetella pertussis and Bordetella bronchiseptica are pathogenic bacteria responsible for respiratory diseases in mammals, including humans. B. pertussis causes whooping cough in humans, primarily affecting young children. Vaccines against B. pertussis consisting of whole-cell inactivated bacteria were introduced globally in the 1940s, leading to a significant decline in pertussis cases. However, these vaccines had undesired side effects such as fever and convulsions. Concerns regarding the safety of these vaccines resulted in their replacement by acellular vaccines in many high-income countries. Although the acellular vaccines were proven to be effective and presented reduced adverse reactions, the number of pertussis cases has been rising during the past decades in the countries using them. B. bronchiseptica causes respiratory diseases in various mammalian species, including dogs and pigs, and can also infect humans with weakened immune systems. Similar to B. pertussis, whole-cell vaccines against B. bronchiseptica have side effects that impact animal welfare and food production. The outer membrane of Gram-negative bacteria, including B. pertussis and B. bronchiseptica, contains lipopolysaccharides (LPS) that are responsible for the toxic immunological response during infection (endotoxicity), and its presence in whole-cell vaccines seems to be the main reason for the undesired side effects produced by these formulations. LPS activates the Toll-like receptor 4 (TLR4), which leads to inflammation and, in extreme cases, to septic shock and death. LPS consists of three major components: lipid A, core oligosaccharide, and O-antigen. Lipid A anchors LPS into the bacterial membrane and is responsible for its endotoxic activity. Modifications to the structure of LPS can affect its ability to stimulate TLR4 and its endotoxicity. The development of novel whole-cell vaccines that are genetically detoxified by LPS bioengineering has been on the rise over the last decades because it allows for the production of affordable and effective vaccines with fewer side effects. In this thesis, we sought to reduce whole-cell endotoxicity in B. pertussis and B. bronchiseptica by genetic modifications that altered the LPS structure or decreased LPS levels. We also investigated the consequences of these modifications on the biology of the bacteria.