Contents Preface v Guest Editors vii Introduction ix List of abbreviations xii 1. Sampling 1 Robert P. Dickson and Michael J. Cox 2. Techniques: culture, identification and 16S rRNA gene sequencing 18 Gisli G. Einarsson and Sébastien Boutin 3. Applying clinical metagenomics for the detection and characterisation 35 of respiratory infections Themoula Charalampous, Gemma L. Kay and Justin O’Grady 4. Applying ecological theories in research: lessons learned 50 from microbial ecology and evolution? Bärbel Ulrike Foesel, Stefan Pfeiffer, Abilash Chakravarthy Durai Raj, Susanne Krauss Etschmann and Michael Schloter 5. The early-life microbiome: the key to respiratory health? 67 Emma M. de Koff, Celine Pattaroni, Benjamin J. Marsland and Debby Bogaert 6. From culturomics to metagenomics: the mycobiome in chronic 88 respiratory diseases Louise-Eva Vandenborght, Raphaël Enaud, Noémie Coron, David Denning and Laurence Delhaes 7. Viruses 119 William G. Flight, Christopher J.R. Turkington and Martha R.J. Clokie 8. Obstructive airways disease: potential pathogenetic roles 140 Kian Fan Chung, Gary B. Huffnagle and Yvonne J. Huang 9. Chronic suppurative lung disease: cystic fibrosis and 158 non-cystic fibrosis bronchiectasis Geraint Rogers and Yvonne J. Huang ERS monograph The Lung Microbiome Number 83 March 2019