The microbiome in respiratory medicine: current challenges and future perspectives

Abstract

The healthy lung has previously been considered to be a sterile organ because standard microbiological culture techniques consistently yield negative results. However, culture-independent techniques report that large numbers of microorganisms coexist in the lung. There are many unknown aspects in the field, but available reports show that the lower respiratory tract microbiota: 1) is similar in healthy subjects to the oropharyngeal microbiota and dominated by members of the Firmicutes, Bacteroidetes and Proteobacteria phyla; 2) shows changes in smokers and well-defined differences in chronic respiratory diseases, although the temporal and spatial kinetics of these changes are only partially known; and 3) shows relatively abundant non-cultivable bacteria in chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, cystic fibrosis and bronchiectasis, with specific patterns for each disease. In all of these diseases, a loss of diversity, paralleled by an over-representation of Proteobacteria (dysbiosis), has been related to disease severity and exacerbations. However, it is unknown whether dysbiosis is a cause or a consequence of the damage to bronchoalveolar surfaces.Finally, little is known about bacterial functionality and the interactions between viruses, fungi and bacteria. It is expected that future research in bacterial gene expressions, metagenomics longitudinal analysis and host-microbiome animal models will help to move towards targeted microbiome interventions in respiratory diseases.

RESPIRE: breathing new life into bronchiectasis

“…This results in marked differences in outcomes and treatment responses even within groups classified by a single feature, such as the presence of P. aeruginosa [19]. Future clinical trials for bronchiectasis must consider patient stratification and selection more closely including potential delineation based on airway inflammation and/ or specific components of the lung microbiome [11,[20][21][22]. A systems biology and multi-omics approach, now more widely accessible, presents an opportunity for bronchiectasis, an opportunity to combine these measures with existing clinical, immunological, microbiological and radiological data to achieve a clearer endo-phenotype for an individual patient.…”

Microbiome in Chronic Lung Diseases

“…Imbalance of the airway microbiome may lead to maladaptive host responses that predispose individuals to chronic lung disease. We are only beginning to understand the functional implications of this dysbiosis and its contribution to disease progression, precipitation of exacerbations and impact on therapeutic interventions in chronic lung diseases 82 . Increasing application of new techniques such as whole genome sequencing and metatranscriptomics with larger cohorts sampled over longer time periods should provide us greater insights.…”

Composition of airway bacterial community correlates with chest HRCT in adults with bronchiectasis

“…Bronchiectasis (BE) not caused by cystic fibrosis (CF) is a debilitating illness with symptoms of recurrent cough, daily sputum production, recurrent chest infections and poor health‐related quality of life (HRQoL) . Patients are frequently chronically infected with bacterial pathogens . Chronic and polymicrobial airway infection contributes to the underlying pathogenesis of the disease, with progressive lung damage resulting from recurrent bacterial infections and inflammatory responses .…”