The respiratory tract is a complex organ system responsible for oxygen and carbon dioxide exchange. It is inhabited by niche-specific bacterial communities that may act as a gatekeeper, preventing colonization by pathogens and maintaining respiratory health. The microbiota of the respiratory tract, including the upper (URT) and lower (LRT) respiratory tracts, plays a crucial role in the maturation and maintenance of respiratory physiology and immunity. Recent research has focused on the ecological and environmental factors that shape these microbial communities and their impact on respiratory health. The URT includes the anterior nares, nasal passages, paranasal sinuses, nasopharynx, and oropharynx, while the LRT includes the larynx, trachea, bronchi, bronchioles, and alveoli. The URT is colonized by specialized bacterial communities, with the highest bacterial densities observed in the URT. These communities may prevent respiratory pathogens from establishing infections and spreading to the LRT. The concept of 'colonization resistance' is central to respiratory health, as it prevents pathogens from overgrowing and causing inflammation. The development of the respiratory microbiota begins in utero and is influenced by factors such as birth mode, feeding type, and environmental exposure. Breastfeeding and vaginal birth are associated with a more health-promoting microbiota profile. Antibiotic use can disrupt the microbiota, increasing the risk of respiratory infections. The microbiota is also influenced by factors such as season, vaccination, and exposure to smoke. The URT microbiota includes a diverse range of bacteria, viruses, and fungi, with species such as Staphylococcus, Corynebacterium, and Moraxella being common. The LRT microbiota is less well understood, but studies suggest it is dominated by species such as Streptococcus and Veillonella. The microbiota in the LRT is thought to be transient and derived from the URT. The microbiota plays a role in immune homeostasis, with interactions between the microbiota and the host influencing immune responses. The microbiota may also modulate the growth of other microorganisms through direct or indirect interactions. The virome and mycobiome also contribute to respiratory health, with interactions between viruses, bacteria, and fungi playing a role in maintaining balance. The respiratory microbiota is essential for the development of the immune system, particularly in early life. The presence of a diverse microbiota in the URT is crucial for the development of lymphoid tissue and immune tolerance. The microbiota may also influence the development of regulatory T cells and the balance between the host, microbiota, and environment. Overall, the respiratory microbiota plays a critical role in maintaining respiratory health, with interactions between the microbiota and the host influencing immune responses and disease susceptibility. Further research is needed to fully understand the complex interactions between the microbiota and the host in the respiratory tract.The respiratory tract is a complex organ system responsible for oxygen and carbon dioxide exchange. It is inhabited by niche-specific bacterial communities that may act as a gatekeeper, preventing colonization by pathogens and maintaining respiratory health. The microbiota of the respiratory tract, including the upper (URT) and lower (LRT) respiratory tracts, plays a crucial role in the maturation and maintenance of respiratory physiology and immunity. Recent research has focused on the ecological and environmental factors that shape these microbial communities and their impact on respiratory health. The URT includes the anterior nares, nasal passages, paranasal sinuses, nasopharynx, and oropharynx, while the LRT includes the larynx, trachea, bronchi, bronchioles, and alveoli. The URT is colonized by specialized bacterial communities, with the highest bacterial densities observed in the URT. These communities may prevent respiratory pathogens from establishing infections and spreading to the LRT. The concept of 'colonization resistance' is central to respiratory health, as it prevents pathogens from overgrowing and causing inflammation. The development of the respiratory microbiota begins in utero and is influenced by factors such as birth mode, feeding type, and environmental exposure. Breastfeeding and vaginal birth are associated with a more health-promoting microbiota profile. Antibiotic use can disrupt the microbiota, increasing the risk of respiratory infections. The microbiota is also influenced by factors such as season, vaccination, and exposure to smoke. The URT microbiota includes a diverse range of bacteria, viruses, and fungi, with species such as Staphylococcus, Corynebacterium, and Moraxella being common. The LRT microbiota is less well understood, but studies suggest it is dominated by species such as Streptococcus and Veillonella. The microbiota in the LRT is thought to be transient and derived from the URT. The microbiota plays a role in immune homeostasis, with interactions between the microbiota and the host influencing immune responses. The microbiota may also modulate the growth of other microorganisms through direct or indirect interactions. The virome and mycobiome also contribute to respiratory health, with interactions between viruses, bacteria, and fungi playing a role in maintaining balance. The respiratory microbiota is essential for the development of the immune system, particularly in early life. The presence of a diverse microbiota in the URT is crucial for the development of lymphoid tissue and immune tolerance. The microbiota may also influence the development of regulatory T cells and the balance between the host, microbiota, and environment. Overall, the respiratory microbiota plays a critical role in maintaining respiratory health, with interactions between the microbiota and the host influencing immune responses and disease susceptibility. Further research is needed to fully understand the complex interactions between the microbiota and the host in the respiratory tract.