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.
The upper respiratory tract is constantly exposed to airborne microbes, many of which are trapped by mucus and removed by immune defenses.
The anterior nares are typically dominated by commensal Staphylococci and Corynebacterium, which can competitively inhibit potential pathogens.
Deeper regions of the nasal cavity and the oropharynx host a broader range of bacteria.
Some resident Streptococcus species produce antimicrobial peptides that inhibit the growth of pathogens.
Interestingly, non-typeable Haemophilus influenzae can opportunistically become pathogenic when host defenses are weakened or mucosal barriers are disrupted.
It typically adheres to mucus and to non-ciliated epithelial cells, forming aggregates that mature into biofilms.
These bacterial cells can then contribute to chronic inflammation or localized infection.
The lower respiratory tract harbors transient microbes that enter with inhaled air and from the oropharynx.
Commonly detected genera include Prevotella and Veillonella. Some of these species survive the reactive oxygen species generated by host metabolism using detoxifying enzymes to protect their cellular structures and DNA.
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