The Lung Microbiome

European Respiratory Society Monograph, Vol. 83. 2019
ISBN (electronic): 978-1-84984-102-3
10.1183/2312508X.erm8319

Studying the lung microbiome requires a specialist approach to sampling, laboratory techniques and statistical analysis. This Monograph introduces the techniques used and discusses how respiratory sampling, 16S rRNA gene sequencing, metagenomics and the application of ecological theory can be used to examine the respiratory microbiome. It examines the different components of the respiratory microbiome: viruses and fungi in addition to the more frequently studied bacteria. It also considers a range of contexts from the paediatric microbiome and how this develops to disease of all ages including asthma and chronic obstructive pulmonary disease, chronic suppurative lung diseases, interstitial lung diseases, acquired pneumonias, transplantation, cancer and HIV, and the interaction of the respiratory microbiome and the environment.

Preface Robert Bals, John R. Hurst Eur Respir Monogr 2019; 83: v-vi
Guest Editors Eur Respir Monogr 2019; 83: vii-viii
Introduction Michael J. Cox, Markus J. Ege, Erika von Mutius Eur Respir Monogr 2019; 83: ix-xi
List of abbreviations Eur Respir Monogr 2019; 83: xii
Sampling the lung microbiome Robert P. Dickson, Michael J. Cox Eur Respir Monogr 2019; 83: 1-17
Techniques: culture, identification and 16S rRNA gene sequencing Gisli G. Einarsson, Sébastien Boutin Eur Respir Monogr 2019; 83: 18-34
Applying clinical metagenomics for the detection and characterisation of respiratory infections Themoula Charalampous, Gemma L. Kay, Justin O'Grady Eur Respir Monogr 2019; 83: 35-49
Applying ecological theories in lung microbiome research: lessons learned from microbial ecology and evolution? Bärbel Ulrike Foesel, Stefan Pfeiffer, Abilash Chakravarthy Durai Raj, Susanne Krauss Etschmann, Michael Schloter Eur Respir Monogr 2019; 83: 50-66
The early-life microbiome: the key to respiratory health? Emma M. de Koff, Celine Pattaroni, Benjamin J. Marsland, Debby Bogaert Eur Respir Monogr 2019; 83: 67-87
From culturomics to metagenomics: the mycobiome in chronic respiratory diseases Louise-Eva Vandenborght, Raphaël Enaud, Noémie Coron, David Denning, Laurence Delhaes Eur Respir Monogr 2019; 83: 88-118
Viruses and the lung microbiome William G. Flight, Christopher J.R. Turkington, Martha R.J. Clokie Eur Respir Monogr 2019; 83: 119-139
The lung microbiome in obstructive airways disease: potential pathogenetic roles Kian Fan Chung, Gary B. Huffnagle, Yvonne J. Huang Eur Respir Monogr 2019; 83: 140-157
The lung microbiome in chronic suppurative lung disease: cystic fibrosis and non-cystic fibrosis bronchiectasis Geraint Rogers, Yvonne J. Huang Eur Respir Monogr 2019; 83: 158-172
Interstitial lung disease David N. O'Dwyer, Bethany B. Moore, Philip L. Molyneaux Eur Respir Monogr 2019; 83: 173-187
The lung bacterial microbiome in community-acquired and nosocomial pneumonia Lieuwe D.J. Bos, Jamie Rylance, Stephen B. Gordon Eur Respir Monogr 2019; 83: 188-194
Compromised immunity and the microbiome: transplantation, cancer and HIV Eric Bernasconi, John-David Aubert, Angela Koutsokera, Laurent P. Nicod, Homer L. Twigg III Eur Respir Monogr 2019; 83: 195-215
The environmental microbiota and asthma Pirkka V. Kirjavainen, Heidi Hyytiäinen, Martin Täubel Eur Respir Monogr 2019; 83: 216-239
Challenges, impact and the future Michael J. Cox, Markus J. Ege, Erika von Mutius Eur Respir Monogr 2019; 83: 240-244