The Lung Microbiome - ERS Monograph: Techniques: culture, identification and 16S rRNA gene sequencing

Gisli Einarsson, Sébastien Boutin

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)peer-review

4 Citations (Scopus)


The resident airway microbiota plays an important role in both health and complex respiratory disorders, including CF, bronchiectasis, COPD and asthma which are characterised by recurrent lung infections and an alteration in innate and adaptive immunity. Recurrent cycles of infection and bronchial inflammation progressively lead to lung injury and long-term damage, and it is therefore imperative to better understand the aetiology of the infective micro-organisms to allow appropriate treatment steps to be implemented. The most prevalent pathogenic bacteria detected in the airways of people with chronic respiratory disease are Haemophilus influenzae, Pseudomonas aeruginosa, Burkholderia cepacia complex, Streptococcus pneumoniae, Staphylococcus aureus and Moraxella catarrhalis, although a number of other potentially pathogenic micro-organisms (PPM) have been proposed to play a role during infective episodes. Variations in the sampling techniques and detection methods used can influence the isolation rates of PPM; it is therefore important to assess the most informative approaches used to identify all clinically relevant micro-organisms. This chapter describes various culture-dependent and -independent methodologies that are currently being employed in an effort to detect and identify the resident microbiota in clinical specimens. It also considers how these methodologies may affect clinical decision-making in the future.
Original languageEnglish
Title of host publicationERS Monograph
Subtitle of host publicationThe Lung Microbiome
EditorsMichael J. Cox, Markus J. Ege, Erika von Mutius
Number of pages34
ISBN (Electronic)978-1-84984-102-3
Publication statusPublished - 2019

Publication series

NameERS Monograph
PublisherEuropean Respiratory Society


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