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Sébastien Boutin [1; 2] and Martin Depner [3] and Mirjam Stahl [2; 4; 5] and Simon Y. Graeber [2; 4; 5] and Susanne A. Dittrich [2; 5; 6] and Antje Legatzki [3] and Erika von Mutius [3] and Marcus Mall [2; 4; 5] and Alexander H. Dalpke [1; 2]

Academic Editor: Pierre-Régis Burgel

1, Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany, heidelberg-university-hospital.com

2, Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany, dzl.de

3, Dr. von Hauner Children’s Hospital, LMU Munich, Munich, Germany, uni-muenchen.de

4, Division of Pediatric Pulmonology and Allergy and Cystic Fibrosis Center, Department of Pediatrics, University Hospital Heidelberg, Heidelberg, Germany, heidelberg-university-hospital.com

5, Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany, uni-heidelberg.de

6, Department of Pneumology and Critical Care Medicine, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany, heidelberg-university-hospital.com

Received May 30, 2017; Revised Aug 24, 2017; Accepted Oct 22, 2017

This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

1. Introduction

Since their emergence, prokaryotes colonize all niches from the extremophilic ones to eukaryotic hosts. One of those niches, long time considered sterile, is the lower airways and the lungs of humans [1]. Of note, even a century ago, it was acknowledged that the lungs are under constant exposure to microorganisms contained in inhaled air and the upper respiratory tract [2]. The conclusion of sterility of the lower airways was based on negative results from standard microbiology that however favors the growth of pathogenic bacteria and was not designed to capture the full spectrum of bacterial species (especially anaerobes) [1].

Airway microbiology is still at the beginning of being deciphered, yet with the advances of research and next-generation sequencing, it is now established that the lower airways in healthy subjects are colonized by bacteria from the oropharyngeal microbiota dominated by members of the Firmicutes, Bacteroidetes, and Proteobacteria phyla [1]. Those findings were the keystone of a theory on the acquisition of the airways’ microbiome which is based on the island model: the lower airways’ (“islands”) microbiota is the result of the colonization from the upper airways (“mainland”) regulated by the elimination...

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