The University of Manchester Research Sputum microbiome temporal variability and dysbiosis in chronic obstructive pulmonary disease exacerbations: an analysis of the COPDMAP study DOI: 10.1136/thoraxjnl-2017-210741 Document Version Accepted author manuscript Link to publication record in Manchester Research Explorer Citation for published version (APA): Kolsum, U., Singh, D., & COPDMAP (2017). Sputum microbiome temporal variability and dysbiosis in chronic obstructive pulmonary disease exacerbations: an analysis of the COPDMAP study. Thorax. https://doi.org/10.1136/thoraxjnl-2017-210741 Published in: Thorax Citing this paper Please note that where the full-text provided on Manchester Research Explorer is the Author Accepted Manuscript or Proof version this may differ from the final Published version. If citing, it is advised that you check and use the publisher's definitive version. General rights Copyright and moral rights for the publications made accessible in the Research Explorer are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Takedown policy If you believe that this document breaches copyright please refer to the University of Manchester’s Takedown Procedures [http://man.ac.uk/04Y6Bo] or contact [email protected] providing relevant details, so we can investigate your claim. Download date:11. Oct. 2021 1 Sputum microbiome temporal variability and dysbiosis in chronic obstructive pulmonary 2 disease exacerbations: an analysis of the COPDMAP study 3 4 Zhang Wang1†, Richa Singh4†, Bruce E. Miller2, Ruth Tal-Singer2, Stephanie Van Horn3, Lynn 5 Tomsho3, Alexander Mackay4, James P. Allinson4, Adam J. Webb5, Anthony J. Brookes5, Leena 6 M. George6, Bethan Barker6, Umme Kolsum7, Louise E Donnelly4, Kylie Belchamber4, Peter J. 7 Barnes4, Dave Singh7, Christopher E. Brightling6, Gavin C. Donaldson4, Jadwiga A. Wedzicha4, 8 James R. Brown1* on behalf of COPDMAP 9 10 1 Computational Biology, Target Sciences, Research and Development (R&D), GlaxoSmithKline 11 (GSK), Collegeville, PA 19426, USA 12 2 Respiratory Therapy Area Unit, R&D, GSK, King of Prussia, PA 19406, USA 13 3 Target and Pathway Validation, Target Sciences, R&D, GSK, Collegeville, PA 19426, USA 14 4 National Heart and Lung Institute, Imperial College London, London, SW3 6NP, UK 15 5 Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK 16 6 Institute for Lung Health, University of Leicester, Leicester, LE3 9QP, UK 17 7 University of Manchester and University Hospital of South Manchester, Manchester, M23 9QZ, 18 UK 19 20 † These authors contributed equally to the manuscript. 21 22 * Correspondence to: 23 James R. Brown ([email protected]) 24 1250 S. Collegeville Road, Collegeville, Pennsylvania, 19426-0989, United States 25 Mobile: +16102478580 26 Tel: +16109176374 27 28 Word count abstract: 240 29 Word count text body: 3500 30 1 31 Abstract 32 Background 33 Recent studies suggest that lung microbiome dysbiosis, the disease associated disruption of the 34 lung microbial community, might play a key role in chronic obstructive pulmonary disease 35 (COPD) exacerbations. However, characterizing temporal variability of the microbiome from 36 large longitudinal COPD cohorts is needed to better understand this phenomenon. 37 38 Methods 39 We performed a 16S ribosomal RNA survey of microbiome on 716 sputum samples collected 40 longitudinally at baseline and exacerbations from 281 COPD subjects at three UK clinical 41 centers as part of the COPDMAP consortium. 42 43 Results 44 The microbiome composition was similar among centers and between stable and exacerbations 45 except for a small significant decrease of Veillonella at exacerbations. The abundance of 46 Moraxella was negatively associated with bacterial alpha diversity. Microbiomes were distinct 47 between exacerbations associated with bacteria versus eosinophilic airway inflammation. 48 Dysbiosis at exacerbations, measured as significant within subject deviation of microbial 49 composition relative to baseline, was present in 41% of exacerbations. Dysbiosis was associated 50 with increased exacerbation severity indicated by a greater fall in FEV1, FVC and a greater 51 increase in CAT score, particularly in exacerbations with concurrent eosinophilic inflammation. 52 There was a significant difference of temporal variability of microbial alpha and beta diversity 53 among centers. The variation of beta diversity significantly decreased in those subjects with 54 frequent exacerbations. 55 56 Conclusions 57 Microbial dysbiosis is a feature of some exacerbations and its presence, especially in concert 58 with eosinophilic inflammation, is associated with more severe exacerbations indicated by a 59 greater fall in lung function. 60 2 61 Key messages: 62 What is the key question? 63 How does the lung microbial community vary over time within COPD subjects and how is 64 microbial dysbiosis in exacerbations implicated in disease characteristics? 65 66 What is the bottom line? 67 Dysbiosis of the sputum microbiome in COPD exacerbations, particularly in concert with 68 eosinophilic inflammation, is associated with a greater decline in lung capacity during the 69 exacerbation event. 70 71 Why read on? 72 The presented study entails the largest COPD sputum microbiome cohort to date with multiple 73 study centers, aiming at in-depth examination of microbial temporal variability, dysbiosis, and 74 disease phenotypes. 3 75 Introduction 76 Chronic obstructive pulmonary disease (COPD) is characterized by persistent symptoms and 77 impaired lung function as a consequence of small airway obliteration and alveolar destruction, 78 and is associated with chronic lung inflammation 1-3. Acute exacerbations of COPD are a sudden 79 onset of sustained worsening of these symptoms. Bacteria potentially play a key role in COPD 80 pathogenesis 4 5, with respiratory bacterial pathogens such as Haemophilus influenzae, Moraxella 81 catarrhalis and Streptococcus pneumoniae capable of driving host inflammatory responses 6-9. 82 Since bacteria frequently interact with each other and respond to altered environmental 83 conditions, the consortium of the lung microbial community, known as the lung microbiome, 84 could be important in the crosstalk between respiratory tract pathogens and host response 10 11. 85 86 Emerging studies collectively suggest that the lung microbiome differs between stable and 87 exacerbations in COPD (11-15, for review see 16). For example, Molyneaux et al. found an 88 increased representation of pathogenic Proteobacteria in particular Haemophilus in 89 exacerbations following rhinovirus infection 12. Huang et al. observed an increase of 90 Proteobacteria during exacerbations with a predicted loss of function in maintenance of 91 microbial homeostasis 13. Recently, several of us published a longitudinal analysis of the sputum 92 microbiome from 87 subjects from BEAT-COPD cohort 11. Our analysis revealed an increased 93 Proteobacteria versus Firmicutes during exacerbations. In addition, we found distinct 94 microbiome composition between bacterial and eosinophilic exacerbations. In light of the 95 heterogeneous nature of COPD exacerbations, the lung microbiome has potential as a biomarker 96 to assist in the precision medicine treatments for specific COPD patient subpopulations. 97 98 Although insightful, results from these previous studies have limitations in terms of 99 understanding microbial dysbiosis during exacerbations, as most of these studies comparing the 100 microbiome at stable and exacerbations involved only one single sampling point of each state. 101 The lung microbiome is temporally dynamic and can vary even in stable state 10.Thus the 102 microbial changes during exacerbations are a mixture of both the disease associated disruption of 103 microbial community or dysbiosis, and the regular temporal perturbations of the lung microbial 104 composition. Therefore, examining the baseline variation of the lung microbiome is an important 4 105 first step to more precisely assess the extent of microbial dysbiosis during exacerbations. On the 106 other hand, understanding temporal variability of the lung microbiome within individuals is also 107 important in disease understanding. Disorder of the temporal balance of microbial ecosystem in 108 the respiratory tract could trigger a dysregulated host immune response that results in negative 109 effects on host biology 10. Linking microbial temporal variation to disease characteristics and 110 host inflammatory profiles could potentially lead to monitoring and manipulating the stability of 111 airway microbial composition as a therapeutic strategy for COPD. 112 113 A finer-grained longitudinal sampling of microbiome at multiple stable and exacerbation visits is 114 necessary to quantitatively measure temporal variability of the microbiome and assess the 115 significance of microbial dysbiosis during exacerbations. Here we describe a longitudinal 16S 116 ribosomal RNA (rRNA) gene based microbiome survey on 716 sputum samples collected 117 sequentially at baseline and exacerbations over a period of up to two years duration from 281 118 COPD subjects at three UK centers as part of the COPDMAP consortium. This entails one of the 119 largest COPD sputum microbiome cohorts to date aiming at in-depth examination of temporal 120 variability of the microbiome. We provide new insights into temporal