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Original article
Microbial communities in the respiratory tract of patients with interstitial lung disease
  1. Christian Garzoni1,2,3,
  2. Silvio D Brugger1,4,
  3. Weihong Qi5,
  4. Sarah Wasmer1,
  5. Alexia Cusini1,2,
  6. Philippe Dumont6,7,
  7. Meri Gorgievski-Hrisoho1,
  8. Kathrin Mühlemann1,2,
  9. Christophe von Garnier6,
  10. Markus Hilty1,2
  1. 1Institute for Infectious Diseases, University of Bern, Bern, Switzerland
  2. 2Department of Infectious Diseases, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
  3. 3Departments of Internal Medicine and Infectious Diseases, Clinica Luganese, Lugano, Switzerland
  4. 4Department of General Internal Medicine, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
  5. 5Functional Genomics Centre, Swiss Federal Institute of Technology and University of Zurich, Zurich, Switzerland
  6. 6Pulmonary Medicine, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
  7. 7HFR Fribourg—Hôpital Cantonal, Fribourg, Switzerland
  1. Correspondence to Dr Markus Hilty, Institute for Infectious Diseases, University of Bern, Friedbühlstrasse 51, Bern CH-3010, Switzerland; Markus.Hilty{at}


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.

  • Sarcoidosis
  • Immunodeficiency
  • Bacterial Infection
  • Respiratory Infection

This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 3.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See:

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