title: 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.
authors.affiliation: Hospital Clinic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain.|CIBER de Enfermedades Respiratorias - CIBERES, Madrid, Spain.|These co-primary authors contributed equally to this work.
authors.forename: Rosa
authors.initials: R
authors.lastname: Faner
authors.affiliation: Hospital Universitari de la Santa Creu i Sant Pau, Universitat Autónoma Barcelona, Barcelona, Spain.|These co-primary authors contributed equally to this work.
authors.forename: Oriol
authors.initials: O
authors.lastname: Sibila
authors.affiliation: Hospital Clinic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain.|CIBER de Enfermedades Respiratorias - CIBERES, Madrid, Spain.
authors.forename: Alvar
authors.initials: A
authors.lastname: Agustí
authors.affiliation: Service de Pneumologie, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
authors.forename: Eric
authors.initials: E
authors.lastname: Bernasconi
authors.affiliation: University of Dundee, Dundee, UK.
authors.forename: James D
authors.initials: JD
authors.lastname: Chalmers
authors.affiliation: University of Michigan, Ann Arbor, MI, USA.
authors.forename: Gary B
authors.initials: GB
authors.lastname: Huffnagle
authors.affiliation: Dept of Gastroenterology, Vall d'Hebron Research Institute, Barcelona, Spain.|CIBER de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain.
authors.forename: Chaysavanh
authors.initials: C
authors.lastname: Manichanh
authors.affiliation: Royal Brompton Hospital, London, UK.
authors.forename: Philip L
authors.initials: PL
authors.lastname: Molyneaux
authors.affiliation: Hospital Universitari Germans Trias i Pujol, Universitat Autónoma Barcelona, Barcelona, Spain.
authors.forename: Roger
authors.initials: R
authors.lastname: Paredes
authors.affiliation: CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.|Joint Research Unit on Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health) and Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain.
authors.forename: Vicente
authors.initials: V
authors.lastname: Pérez Brocal
authors.affiliation: Centro de Regulación Genómica, Barcelona, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Julia
authors.initials: J
authors.lastname: Ponomarenko
authors.affiliation: University of Buffalo, Buffalo, NY, USA.
authors.forename: Sanjay
authors.initials: S
authors.lastname: Sethi
authors.affiliation: Hospital Universitari de Bellvitge, IDIBELL, Universitat de Barcelona, Hospitalet del Llobregat, Barcelona, Spain.|These co-senior authors contributed equally to this work.
authors.forename: Jordi
authors.initials: J
authors.lastname: Dorca
authors.affiliation: CIBER de Enfermedades Respiratorias - CIBERES, Madrid, Spain emonso@tauli.cat.|Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, Barcelona, Spain.|These co-senior authors contributed equally to this work.
authors.forename: Eduard
authors.initials: E
authors.lastname: Monsó
mesh_terms: D000818:Animals; D041963:Bacteroidetes / Q000145:classification*; D001987:Bronchiectasis / Q000382:microbiology; D003550:Cystic Fibrosis / Q000382:microbiology; D064806:Dysbiosis; D054884:Host-Pathogen Interactions; D006801:Humans; D054988:Idiopathic Interstitial Pneumonias / Q000382:microbiology; D008168:Lung / Q000382:microbiology*; D051379:Mice; D064307:Microbiota; D020560:Proteobacteria / Q000145:classification*; D029424:Pulmonary Disease, Chronic Obstructive / Q000382:microbiology; D015272:Pulmonary Medicine; D012307:Risk Factors; D009626:Terminology as Topic