Table I. Factors that impact the lung microbiota during acute and chronic disease
Influences
Architectural
 Airway obliteration (lung transplant, IPF)
 Terminal bronchiole destruction (COPD)
 Honeycombing and fibrosis (IPF)
 Impaired mucociliary clearance (COPD, asthma)
Immunologic
 Innate immune cell impairment
 Altered PRR signaling
 Release of antimicrobial peptides
 Apoptosis/autophagy
 Inflammation
 Cytokine alterations
Microbiologic
 Overgrowth of limited bacterial species (IPF, CF)
 Antibiotic use (especially in CF)
 Lytic viral infection (COPD, asthma)
 Latent viral infection (IPF?)
 Biofilm formation (CF, COPD)
Pathologic
 Osmotic changes (CF)
 Thickened mucus (CF)
 Damaged cilia (COPD)
 Changes in oxygen tension, ventilation, and perfusion (IPF, COPD, CF, asthma)
 Microaspiration (IPF)