ERS | monograph Introduction Michael J. Cox1, Markus J. Ege2,3 and Erika von Mutius2,3,4 @ERSpublications The lung microbiome is an emerging context for respiratory disease. This book: introduces the field discusses methodology consolidates knowledge of the influence of microbial communities considers new developments and discusses therapeutic use. http://ow.ly/1oSD30nGD0Z In constant contact with the wider environment, the respiratory tract and lungs are continually exposed to micro-organisms. It has been demonstrated, using both culture-independent and -dependent techniques that there are microbial communities in the healthy LRT. The findings have been remarkably consistent and particular organisms are common to this environment and differ between health and disease in both the number and particular types of organism. Different communities of bacteria are present in different diseases, and in different disease states. We are beginning to understand the early development of the lung microbiome, which accrues organisms as infants grow. Selection by the host environment and immune system also play a part, as it is not a random collection of environmental organisms that can be found but a reproducible subset. There are interactions between the lung microbiome, the oral microbiome and the gut microbiome that may significantly shape the microbiome of the lower airways these interactions are currently being explored. Respiratory diseases are amongst the most common causes of morbidity and mortality worldwide and whether acute or chronic, micro-organisms are involved in all of them. This can be in susceptibility to disease, in its cause, in inflammation, in response to disease or in response to treatment. Though much progress has been made in the last decade, these processes are not well understood in the context of the microbiome. Studying the lung microbiome requires specialist approaches to sampling, laboratory techniques and statistical analysis against the background of a rapidly developing field, which tends to focus on more easily studied host environments, such as the gut. In this Monograph, we introduce the techniques used and how respiratory sampling [1], 16S rRNA gene sequencing [2], metagenomics [3] and the application of ecological theory [4] can be used to examine the respiratory microbiome experimentally. Following this, we examine different Copyright ©ERS 2019. Print ISBN: 978-1-84984-101-6. Online ISBN: 978-1-84984-102-3. Print ISSN: 2312-508X. Online ISSN: 2312-5098. Correspondence: Michael J. Cox, Section of Genomic Medicine, National Heart and Lung Institute, Guy Scadding Building, Royal Brompton Campus, London, SW3 6LY, UK. E-mail: michael.cox1@imperial.ac.uk 1 National Heart and Lung Institute, Imperial College London, London, UK. 2 Dept of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany. 3 Comprehensive Pneumology Center Munich, Member of the German Center for Lung Research, Munich, Germany. 4 Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Institute for Asthma and Allergy Prevention, Neuherberg, Germany. https://doi.org/10.1183/2312508X.10012119 ix