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Title The microbiome in respiratory medicine: current challenges and future perspectives

Authors Rosa Faner, Oriol Sibila, Alvar Agustí, Eric Bernasconi, James D. Chalmers, Gary B. Huffnagle, Chaysavanh Manichanh, Philip L. Molyneaux, Roger Paredes, Vicente Pérez Brocal, Julia Ponomarenko, Sanjay Sethi, Jordi Dorca, Eduard Monsó
Date 04 2017

Publisher The European Respiratory Journal
DOI 10.1183/13993003.02086-2016
Tag Animals, Bacteroidetes, Bronchiectasis, Cystic Fibrosis, Dysbiosis, Host-Pathogen Interactions, Humans, Idiopathic Interstitial Pneumonias, Lung, Mice, Microbiota, Proteobacteria, Pulmonary Disease, Chronic Obstructive, Pulmonary Medicine, Risk Factors, Terminology as Topic

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.

Annotation CRG collaborates with the Hospital San Pau, Hospital Clinic, Hospital del Mar and other institutions in Barcelona, which are part of the Barcelona Respiratory Network on studies of the lung microbiomes in patients affected by chronic obstructive pulmonary disease (COPD). The BioCore contribution is the analysis of 16S rRNA sequencing data.
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