Lung Microbiome for Clinicians. New Discoveries about Bugs in Healthy and Diseased Lungs

Abstract

Microbes are readily cultured from epithelial surfaces of the skin, mouth, and colon. In the last 10 years, culture-independent DNAbased techniques demonstrated that much more complex microbial communities reside on most epithelial surfaces; this includes the lower airways, where bacterial culture had failed to reliably demonstrate resident bacteria. Exposure to a diverse bacterial environment is important for adequate immunological development. The most common microbes found in the lower airways are also found in the upper airways. Increasing abundance of oral characteristic taxa is associated with increased inflammatory cells and exhaled nitric oxide, suggesting that the airway microbiome induces an immunological response in the lung. Furthermore, rhinovirus infection leads to outgrowth of Haemophilus in patients with chronic obstructive pulmonary disease, and human immunodeficiency virus-infected subjects have more Tropheryma whipplei in the lower airway, suggesting a bidirectional interaction in which the host immune defenses also influence the microbial niche. Quantitative and/or qualitative changes in the lung microbiome may be relevant for disease progression and exacerbations in a number of pulmonary diseases. Future investigations with longitudinal follow-up to understand the dynamics of the lung microbiome may lead to the development of new therapeutic targets.

Role of infection in exacerbations of chronic obstructive pulmonary disease

“…Sputum culture has traditionally been used for the identification of bronchial infection by bacteria; however, currently available techniques are not suitable for the identification of up to 80% of microorganisms inhabiting mucosal surfaces [39]. In this context, molecular culture independent techniques have identified bacteria previously not amenable to culture.…”

Relevance of Systems Biology to Respiratory Medicine

“…To address this complexity, systems biology approaches will be needed. In fact, they have already begun to be applied to several respiratory diseases too [49][50][51][52][53][54][55] .…”

Lungs, Microbes and the Developing Neonate

“…Previously thought to be sterile, data suggest the presence of bacterial DNA in the lower respiratory tract, some of which is similar to that of the upper airway, but some of which appears to be over-represented in the lower airways [10–12]. Although concerns about acquisition and contamination of lower airway specimens through the necessity of traversing the upper airway in humans are present, careful studies comparing the upper and lower airway microbiota, studies using explanted lungs at the time of transplantation and mouse studies have demonstrated that, although present in low numbers in healthy lungs, there is a lower airway microbial presence that is distinct from that of the upper airway [13–17].…”