Respiratory Microbiome

Respiratory Microbiome - Our Breathing Buddies

• Dynamic microbial communities in respiratory tract; crucial for health & disease.
• Upper Respiratory Tract (URT):
  • Nose, nasopharynx, oropharynx, larynx.
  • Higher microbial density & diversity.
  • Dominant genera: Staphylococcus, Streptococcus, Corynebacterium, Dolosigranulum, Moraxella, Haemophilus.
• Lower Respiratory Tract (LRT):
  • Trachea, bronchi, lungs.
  • Low biomass; distinct from URT. Not sterile.
  • Common genera: Prevotella, Veillonella, Streptococcus, Pseudomonas, Haemophilus.
• Key Functions:
  • Immune homeostasis & education.
  • Colonization resistance (pathogen displacement).
• Dysbiosis (Imbalance):
  • Associated with asthma, COPD, cystic fibrosis, pneumonia, ARDS.
  • Influenced by: antibiotics, smoking, pollution, host genetics, infections.

⭐ The "sterile lung" paradigm is outdated; the LRT harbors a distinct, low-density microbiome, critical for respiratory health.

Meet the Microbes - Resident Roster

• Upper Respiratory Tract (URT: Nasopharynx, Oropharynx)
  • High bacterial load & diversity. Key site for initial colonization.
  • Common residents: 📌 Silly Students Hate Micro Class Notes
    • Streptococcus (viridans, S. pneumoniae)
    • Staphylococcus (S. epidermidis, S. aureus - carriage)
    • Haemophilus influenzae (non-typeable)
    • Moraxella catarrhalis
    • Corynebacterium spp. (diphtheroids)
    • Commensal Neisseria spp.
  • Also significant: Anaerobes (Prevotella, Veillonella, Fusobacterium).
• Lower Respiratory Tract (LRT: Trachea, Lungs)
  • Low bacterial biomass; not sterile.
  • Reflects URT via microaspiration & mucociliary clearance.
  • Predominant: Prevotella, Veillonella, Streptococcus.
  • Transient colonizers often cleared by host defenses.
• Clinical Relevance:
  • Alterations (dysbiosis) linked to asthma, COPD, pneumonia.
  • URT commensals can become opportunistic pathogens.

  ⭐ The lungs, once thought sterile, harbor a low-density microbiome in health, largely seeded by URT microaspiration.

Microbial Mayhem - When Balance Breaks

• Dysbiosis: Respiratory microbial imbalance; loss of homeostasis.
  • Hallmarks: ↓ Diversity, ↑ pathobionts (e.g., H. influenzae, S. pneumoniae), ↓ commensals (Prevotella, Veillonella).
• Key Triggers:
  • Antibiotics (esp. broad-spectrum)
  • Viral infections (Influenza, RSV)
  • Host factors: Genetics, immunodeficiency
  • Environment: Smoking, pollutants, aspiration
• Clinical Impact:
  • Asthma/COPD: Exacerbations, ↑ severity.
  • Cystic Fibrosis (CF): Chronic infections (P. aeruginosa), lung function ↓.
  • Pneumonia: ↑ Susceptibility, altered course.
  • Bronchiectasis: Vicious cycle of infection-inflammation.
  • Lung Cancer: Potential contributor.

⭐ In Cystic Fibrosis, Pseudomonas aeruginosa often forms biofilms, contributing to antibiotic resistance and persistent lung infection.

Investigating & Intervening - Future Frontiers

• Investigation Techniques:
  • Next-Gen Sequencing (NGS): 16S rRNA gene, shotgun metagenomics (DNA).
  • Functional 'Omics': Metatranscriptomics (RNA), metabolomics (metabolites).
  • Sampling: Bronchoalveolar lavage (BAL), sputum, nasal swabs.
• Diagnostic Potential:
  • Microbial biomarkers for early disease detection (asthma, COPD, pneumonia).
  • Predicting treatment efficacy.
• Therapeutic Avenues:
  • Modulation: Probiotics, prebiotics, synbiotics.
  • Targeted: Phage therapy, engineered bacteria.
  • Metabolite-based: Postbiotics (e.g., SCFAs).

  ⭐ Alterations in lung microbiome (dysbiosis) are increasingly recognized as key factors in asthma pathogenesis and severity.

• Key Challenges: Standardizing protocols, proving causation, targeted delivery methods for therapeutics to the lungs.

High‑Yield Points - ⚡ Biggest Takeaways

• The respiratory tract, previously thought sterile, hosts a distinct microbiome.
• Upper respiratory tract (URT) has more microbes and greater diversity than the lower respiratory tract (LRT).
• Dominant phyla include Firmicutes, Bacteroidetes, and Proteobacteria.
• Dysbiosis (imbalance) is linked to asthma, COPD, cystic fibrosis, and respiratory infections.
• The lung microbiome is primarily shaped by microaspiration from the URT and elimination via mucociliary clearance.
• Host immunity, antibiotics, and environmental factors significantly modulate the respiratory microbiome.
• Common genera in healthy lungs include Streptococcus, Prevotella, and Veillonella.