Lung Microbiome Diversity, Infection Dynamics, and Microbe-Mediated Cross-Protection

Modern technological advances have revealed that the lungs, once believed to be sterile, actually harbor a diverse community of microorganisms. A normal lung microbiome possesses its own characteristic microbial community, although it is largely influenced by the microbiota of the upper respiratory tract. The lung microbiome is distinct from that of other organs due to unique selective pressures, including mechanical clearance through coughing, the activity of pulmonary macrophages, the coordinated movement of respiratory cilia, and the antimicrobial effects of alveolar surfactant. Although recent research has largely concentrated on the pulmonary bacteriome, comparatively little attention has been given to the lung mycobiome and virome. Various databases such as PubMed, Scopus/Web of Science, Google Scholar, and Medline for literature research up to December 2025. This updated review discusses the origin, composition, and functional significance of the lung microbiome, with particular emphasis on its protective role against respiratory pathogens through host-microbe interactions. The review primarily focuses on respiratory disorders such as asthma, along with a range of viral and bacterial infections. Special attention is given to current evidence on how lung microbial communities influence susceptibility to pulmonary infections, as well as how the lung microbiome contributes to host defense during infectious conditions.