This chapter explores the role of the lung microbiota in maintaining respiratory homeostasis and its interactions with other microbial communities, particularly through the gut-lung axis. Once considered sterile, the lung now hosts a dynamic microbial community influenced by environmental, geographical, and circadian factors. The lung microbiota plays a crucial role in immune regulation by protecting against infections and contributing to the development of diseases such as asthma, chronic obstructive respiratory disorder, and ventilator-associated pneumonia. This chapter also examines how dysbiosis of the lung microbiota is linked to critical conditions like acute respiratory distress syndrome (ARDS) and sepsis, highlighting its connections with both the gut and brain microbiota. The gut-lung axis is discussed in relation to immune modulation, while the brain-lung axis is explored within the context of neuroimmune interactions. Finally, potential therapeutic strategies are presented, including fecal microbiota transplantation, probiotics (particularly Lactobacillus spp.), and microbial metabolites, all of which may help regulate immune responses and prevent respiratory diseases.