Microbial communities in the respiratory tract of patients with interstitial lung disease

Garzoni, Christian; Brugger, Silvio D.; Qi, W.; Wasmer Rueff, Sarah Patricia; Cusini, Alexia; Dumont, P.; Gorgievski, Meri; Mühlemann, Kathrin; Von Garnier, Christophe; Hilty, Markus (2013). Microbial communities in the respiratory tract of patients with interstitial lung disease. Thorax, 68(12), pp. 1150-1156. BMJ Publishing Group 10.1136/thoraxjnl-2012-202917

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Background Molecular methods based on phylogenetic differences in the 16S rRNA gene are able to characterise the microbiota of the respiratory tract in health and disease.

Objectives Our goals were (1) to characterise bacterial communities in lower and upper airways of patients with interstitial lung disease (ILD) and (2) to compare the results with the microbiota of patients with Pneumocystis pneumonia (PCP) and normal controls.

Methods We examined the upper and lower respiratory tract of 18 patients with ILD of whom 5, 6, and 7 had idiopathic interstitial pneumonia (IIP), non-IIP and sarcoidosis, respectively. In addition, six immune-compromised patients with PCP and nine healthy subjects were included as controls. Exclusion criteria were recent bacterial/viral respiratory tract infection, HIV-positivity and subjects receiving antibiotic therapy. Bronchoalveolar lavage fluid and oropharyngeal swabs were simultaneously collected, and microbiota was characterised by ultra-deep 16S rRNA gene sequencing.

Results The microbiota in lower airways of the majority of patients (30; 90%) primarily consisted of Prevotellaceae, Streptococcaceae and Acidaminococcaceae. α and β diversity measurements revealed no significant differences in airway microbiota composition between the five different groups of patients. Comparison of bacterial populations in upper and lower respiratory tract showed significant topographical discontinuities for 7 (23%) individuals.

Conclusions IIP, non-IIP and sarcoidosis are not associated with disordered airway microbiota and a pathogenic role of commensals in the disease process is therefore unlikely. Nevertheless, molecular analysis of the topographical microbiota continuity along the respiratory tract may provide additional information to assist management of individual patients.

Item Type:

Journal Article (Original Article)


04 Faculty of Medicine > Department of General Internal Medicine (DAIM) > Clinic of General Internal Medicine > Centre of Competence for General Internal Medicine
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) > Forschungsbereich Mu50 > Forschungsgruppe Pneumologie (Erwachsene)
04 Faculty of Medicine > Department of Gastro-intestinal, Liver and Lung Disorders (DMLL) > Clinic of Pneumology
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases
04 Faculty of Medicine > Department of Haematology, Oncology, Infectious Diseases, Laboratory Medicine and Hospital Pharmacy (DOLS) > Clinic of Infectiology

UniBE Contributor:

Garzoni, Christian, Brugger, Silvio, Wasmer Rueff, Sarah Patricia, Cusini, Alexia, Gorgievski, Meri, Mühlemann, Kathrin, von Garnier, Christophe, Hilty, Markus


600 Technology > 610 Medicine & health
500 Science > 570 Life sciences; biology




BMJ Publishing Group




Marina Beutler

Date Deposited:

21 Mar 2014 11:44

Last Modified:

02 Mar 2023 23:24

Publisher DOI:






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