The Human Respiratory Microbiome: Implications and Impact

Alicia B. Mitchell, BMedSci (Hons); Allan R. Glanville, MBBS, MD, FRACP


Semin Respir Crit Care Med. 2018;39(2):199-212. 

In This Article

Cystic Fibrosis

It is generally accepted that pathogenic bacteria such as S. aureus and P. aeruginosa are commonly present within the lower airways of patients with CF and almost universally present by adolescence.[70] CF was one of the notable exceptions to the previous understanding that the lungs were sterile. Hence, CF research has led the field in microbiome-related studies in chronic lung diseases.

Microbial composition and diversity vary with disease progression. As patients develop more severe disease, bacterial community diversity has been shown to decrease significantly. However, in individuals with a mild lung disease phenotype, the bacterial community diversity remains stable over time. In both cases, microbial density remained steady. The most significant driver of a microbiome shift was antibiotic usage; however, over time with increased usage, bacterial communities developed resistance to change.[23,25]

Studies have suggested that treatment outcomes do not correlate with the susceptibility of strains of P. aeruginosa to certain antibiotics. Two large trials have shown no association between the clinical response to antibiotics during pulmonary exacerbations and in vitro bacterial susceptibility to the chosen antibiotics.[71,72] This suggests that a single organism may not be responsible for causing an exacerbation. Instead, complex microbiome interactions may be of greater importance.

Multiple studies in CF have shown that there is no change in bacterial burden or community diversity between samples taken during stable periods and at the time of exacerbations. It is instead suggested that an exacerbation occurs when there is an acute dysbiosis of the respiratory microbiome (acute shift in bacterial species) coupled with a disordered host immune response.[25,73–75] Price et al showed that the lung microbiota in CF had a complex microbial composition, which appeared to be unique to each patient analyzed. This microbiome demonstrated resilience to exacerbation and antibiotic treatment with persistence of microbial species observed at multiple time points.[76]

Microbial interactions play an important role in CF exacerbation frequency and progression of the disease. Emerging research is examining the possibility of modifying the microbiome to improve disease-related outcomes for patients with CF.[43,77]