Respiratory tract microbiome

Respiratory Microbiome - The Breathing Buddies

• Upper Respiratory Tract (URT): Dense, diverse community.
  • Nose/Pharynx: Staphylococcus, Streptococcus, Corynebacterium, Neisseria.
• Lower Respiratory Tract (LRT): Previously considered sterile. Now known to have low bacterial biomass, primarily from URT microaspiration.
  • Common genera: Prevotella, Veillonella, Streptococcus.
• Function: Crucial for immune system education and colonization resistance against pathogens.
• Dysbiosis: Imbalance linked to asthma, COPD exacerbations, and ↑ pneumonia risk.

⭐ The trio of Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis are common URT colonizers that can become pathogenic, causing otitis media, sinusitis, and pneumonia, especially post-viral infection.

Tract Topography - Upstairs vs Downstairs

• Upper Respiratory Tract (URT): Nasopharynx, Oropharynx

  • Densely populated, similar to the oral cavity.
  • Common colonizers: Staphylococcus epidermidis, Viridans streptococci, Haemophilus influenzae, Neisseria spp., and Corynebacterium spp. (diphtheroids).
  • Acts as a reservoir for potential pathogens.

• Lower Respiratory Tract (LRT): Trachea, Bronchi, Lungs

  • Traditionally considered sterile; now known to have a low-biomass microbiome.
  • Populated by transient microaspiration from the URT.
  • Predominant genera: Prevotella, Veillonella, and Streptococcus.

⭐ The sterility of the LRT is actively maintained by the mucociliary escalator, which traps and expels microbes, and by alveolar macrophages that clear any organisms reaching the alveoli.

Clinical Correlations - Balance & Battles

• Dysbiosis: The disruption of the stable microbial community, creating a window for opportunistic pathogens (“pathobionts”) to overgrow and cause disease.
• Common Triggers: Viral infections (e.g., Influenza), smoking, broad-spectrum antibiotics, and immunosuppression.
• Key Pathobionts:
  • Streptococcus pneumoniae
  • Haemophilus influenzae
  • Moraxella catarrhalis
  • 📌 Mnemonic: SHiM

⭐ Viral URIs, particularly influenza, damage the respiratory epithelium and impair ciliary function. This paves the way for secondary bacterial pneumonia, most frequently caused by S. pneumoniae.

• The upper respiratory tract (URT) is heavily colonized; the lower respiratory tract (LRT) is kept sterile by the mucociliary escalator.
• Common URT flora include S. pneumoniae, H. influenzae, and N. meningitidis, which can be opportunistic pathogens.
• Staphylococcus aureus colonization in the anterior nares is a major risk factor for endogenous and nosocomial infections.
• Aspiration of this oral/nasal flora is a primary mechanism for developing pneumonia.
• Viral infections disrupt this balance, predisposing to secondary bacterial infections.