Lung microbiota

The lung microbiota is the pulmonary microbial community consisting of a complex variety of microorganisms found in the lower respiratory tract particularly on the mucous layer and the epithelial surfaces. Although the anatomically lower airway were once thought to be sterile, culture-independent molecular technologies have revealed resident and transient microbial communities even in healthy lungs. In contrast to the gut or upper airway, the lung microbial biomass is very low, and its steady state composition is determined less by stable colonization and more by a balance of microbial immigration (for example via micro-aspiration or inhalation) and clearance (for example via mucociliary transport, immune defenses, and alveolar surfactant). In health, this dynamic ecology supports immune homeostasis and may contribute to disease homeostasis and may contribute to disease resistance. In a disease state, shifts in microbial burden, taxonomic composition, diversity, or translocation of non-typical taxa are increasingly recognized in the pathogenesis and prognosis of respiratory disorders (such as chronic obstructive pulmonary disease, asthma, interstitial lung disease, acute respiratory distress syndrome, and lung cancer). As such, the lung microbiota is emerging as potential biomarker and therapeutic target in pulmonary medicine. These microorganisms include bacteria, fungi, viruses and bacteriophages. The bacterial part of the microbiota has been more closely studied. It consists of a core of nine genera: Prevotella, Sphingomonas, Pseudomonas, Acinetobacter, Fusobacterium, Megasphaera, Veillonella, Staphylococcus, and Streptococcus. They are aerobes as well as anaerobes and aerotolerant bacteria. The microbial communities are highly variable in particular individuals and compose of about 140 distinct families. The bronchial tree for instance contains a mean of 2000 bacterial genomes per cm² surface. The harmful or potentially harmful bacteria are also detected routinely in respiratory specimens. The most significant are Moraxella catarrhalis, Haemophilus influenzae, and Streptococcus pneumoniae. They are known to cause respiratory disorders under particular conditions namely if the human immune system is impaired. The mechanism by which they persist in the lower airways in healthy individuals is unknown.

The fungal genera that are commonly found make up the lung mycobiome, in the microbiota of the lung, and include Candida, Malassezia, Neosartorya, Saccharomyces, and Aspergillus, among others.