Microbiota of the Respiratory Tract

The human respiratory tract, comprising the upper and lower segments, serves as a critical interface with the external environment. The upper respiratory tract (URT)—including the nostrils, sinuses, pharynx, and oropharynx—is heavily colonized by microbes, while the lower respiratory tract (LRT), composed of the larynx, trachea, bronchi, and lungs, was long thought to be sterile. However, recent molecular studies have revealed that the lungs are not devoid of microbes but act more like transient reservoirs, with microbial immigration largely from the oropharynx.

The anterior nares resemble skin and support lipophilic Gram-positive bacteria such as Staphylococcus, Corynebacterium, and Cutibacterium. Deeper nasal regions host Streptococcus, Dolosigranulum, Moraxella, and Haemophilus. The oropharynx is the most diverse area, containing both Gram-positive and Gram-negative genera, including Neisseria, Veillonella, and Prevotella. These commensals play roles in suppressing pathogens and supporting mucosal immunity.

The lungs, though less densely colonized, harbor bacteria such as Prevotella, Veillonella, Streptococcus, and Pseudomonas, most of which originate from the mouth. These organisms, often anaerobic, survive in oxygen-rich environments by producing antioxidant enzymes. In individuals with asthma, COPD, or cystic fibrosis, Gram-negative bacteria are more common, and microbes like Nitrosomonas may influence diagnostic markers such as exhaled nitric oxide.

Several infections originate in the URT, including streptococcal pharyngitis caused by Streptococcus pyogenes. This pathogen resists immune clearance and can lead to complications like scarlet fever or otitis media. Diphtheria, caused by Corynebacterium diphtheriae, remains dangerous due to its potent toxin, though vaccines have greatly reduced its prevalence. Otitis media, particularly in children, is often caused by S. pneumoniae, H. influenzae, or Moraxella and may require antibiotics.

Emerging research on the lung microbiome opens new avenues for understanding respiratory health. As the respiratory tract is increasingly seen as a dynamic microbial ecosystem, future therapies may involve targeted manipulation of its microbiota to prevent or manage disease.