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Northumbria Research Link Northumbria Research Link Citation: Purcell, Paul (2013) The characterisation of polymicrobial bacterial communities in the lower respiratory tract of individuals with chronic pulmonary disease. Doctoral thesis, Northumbria University. This version was downloaded from Northumbria Research Link: http://nrl.northumbria.ac.uk/id/eprint/11824/ Northumbria University has developed Northumbria Research Link (NRL) to enable users to access the University’s research output. Copyright © and moral rights for items on NRL are retained by the individual author(s) and/or other copyright owners. Single copies of full items can be reproduced, displayed or performed, and given to third parties in any format or medium for personal research or study, educational, or not-for-profit purposes without prior permission or charge, provided the authors, title and full bibliographic details are given, as well as a hyperlink and/or URL to the original metadata page. The content must not be changed in any way. Full items must not be sold commercially in any format or medium without formal permission of the copyright holder. The full policy is available online: http://nrl.northumbria.ac.uk/policies.html The characterisation of polymicrobial bacterial communities in the lower respiratory tract of individuals with chronic pulmonary disease Paul J. Purcell PhD 2013 The characterisation of polymicrobial bacterial communities in the lower respiratory tract of individuals with chronic pulmonary disease Paul J. Purcell A thesis submitted in partial fulfilment of the requirements of the University of Northumbria at Newcastle for the degree of Doctor of Philosophy Research undertaken in the School of Life Sciences and in collaboration with the Freeman Hospital, Newcastle upon Tyne January 2013 Publications relating to thesis Publications Purcell, P.J., Jary, H., Nicholson, A. Perry, J.D., Lanyon, C., Smith, D., Cummings, S.P., De- Soyza, A. (2012). Polymicrobial airway bacterial communities in adult non-CF bronchiectasis patients (in preparation for submission). Purcell, P.J., Cummings, S.P., Jary, H., De-Soyza, A., & Perry, J.D. (2012). Changes in the lower airway bacterial communities from adult non-CF bronchiectasis populations are significantly associated with exacerbations and the presence of Haemophilus influenzae. European Respiratory Journal 40: Supplement 56: 450s. Purcell, P.J., Nelson, A., Fisher, A., Perry, J.D., De-Soyza, A., & Cummings, S.P. (2011). Molecular fingerprinting and metagenomic analysis reveals a polymicrobial element in patients with chronic obstructive pulmonary disease. Thorax 66: Supplement 4: A11-A12. Cummings, S.P., Nelson, A., Purcell, P.J., De-Soyza, A., Bourke, S.J., & Perry, J.D. (2010). A comparative study of polymicrobial diversity in CF and non-CF bronchiectasis. Thorax 65: Supplement 4: A13-A14. Oral presentations Purcell, P.J., Nelson, A., Fisher, A., Perry, J.D., De-Soyza, A., & Cummings, S.P. (2011). Molecular fingerprinting and metagenomic analysis reveals a polymicrobial element in patients with chronic obstructive pulmonary disease. Presented at the British Thoracic Society Winter Meeting, London, 7th December 2011. Purcell, P.J., Nelson, A., & Cummings, S.P. (2009). Comparison of DNA polymerase enzymes in DGGE studies of bacterial communities in soil. Presented at the 15th Molecular Microbial Ecology Group Meeting, Aberdeen University, 30th July 2009. Poster presentations Purcell, P.J., Cummings, S.P., Jary, H., De-Soyza, A., & Perry, J.D. (2012). Changes in the lower airway bacterial communities from adult non-CF bronchiectasis populations are significantly associated with exacerbations and the presence of Haemophilus influenzae. Presented at the European Respiratory Society Annual Congress Conference, Austria, Vienna, 3rd September 2012. Purcell, P.J., De-Soyza, A., Jary, H., Perry, J.D., Cummings, S.P. (2011). PCR-DGGE mediated studies of non-CF bronchiectasis individuals reveals a polymicrobial community. Presented at the Society for General Microbiology Spring Conference, Harrogate International Centre, 13th April 2011. iii Abstract Microbial diversity encompasses the whole of the Earth’s biosphere and is incredibly vast. The microbial diversity of three disparate micro-environments using two culture-independent techniques (denaturing gradient gel electrophoresis (DGGE) and 454-pyrosequencing) were revealed. Five commercially available DNA polymerase (pol) enzymes were assessed in determining the bacterial community generated in sandy soil. The V3 region of the 16S rRNA gene was targeted for amplification by polymerase chain reaction (PCR). Using a PCR- DGGE approach, different DNA pols exhibited differences in the DGGE profiles produced. Both high-fidelity DNA pols Ex Taq™ Hot Start (HS) and Platinum® Pfx detected greater microbial diversity present within sandy soil than the other DNA polymerase enzymes. We employed Ex Taq™ HS to characterise the microbial communities present in two chronic respiratory tract diseases, non-cystic fibrosis bronchiectasis (nCFBR) and chronic obstructive pulmonary disease (COPD). Seventy individuals expectorated sputum, and using 16S and 28S rRNA PCR-DGGE polymicrobial communities were revealed. From the 70 patients investigated, 20 presented with symptoms consistent with an exacerbation, the remainder being clinically stable. Demographic and culture data were used in constrained ordination analyses to identify any significant associations between these data and changes in the sputum microbiota. The data presented indicates that bacterial lung communities in adult nCFBR patients have distinct differences between exacerbating and clinically stable episodes. Persistent colonisation by Pseudomonas aeruginosa is significantly associated with reduced lung function, and is negatively correlated with Haemophilus influenzae carriage. Bacterial communities seem to be predominantly assembled by stochastic processes. Fungal taxa present were scarce. Stable COPD populations have been previously investigated using culture-dependent techniques. Eleven clinically stable COPD patients had a bronchoalveolar lavage (BAL) fluid taken from the right lower lobe. Both 16S and 28S rRNA PCR-DGGE was performed on all clinical samples from extracted DNA. Co-migration of bands was then compared to a 16S and 28S standard ladder consisting of pure cultivars. Additionally, execution of 454- pyrosequencing and interrogation of the V3-V5 region of 16S rRNA genes resulted in 1799 unique OTUs being identified. Dominant bacterial genera identified were Streptococcus, Arthrobacter, and Staphylococcus respectively. Bacterial taxa identified were then subjected to multivariate statistical analysis to identify relationships between the microbial communities and patient phenotypes. Metagenomic analysis demonstrated that heterogeneous bacterial populations exist in all eleven individuals. This preliminary study shows that the lungs of COPD sufferers are colonised with multiple species of bacteria and demonstrate that a complex microbial community is present. Furthermore, bacterial phylotypes resolved to class-level indicated three potential drivers of community structure within the COPD lung microbiome: lung function, moderate and severe COPD progression, and smoking status in cohort. The identification of a greater number of bacterial taxa was also apparent in culture- negative patients using both PCR-DGGE and 454-pyrosequencing approaches. iv List of tables _____________________________________________________________________________ xi List of figures _____________________________________________________________________________ xii Acknowledgements _______________________________________________________________________ xv List of abbreviations _____________________________________________________________________ xviii Chapter One: General introduction ____________________________________________________________ 1 1.1 A global view of micro-organism biodiversity__________________________________________________ 1 1.2 The origins of modern molecular microbiology ________________________________________________ 2 1.3 Culture-dependent microbiology ___________________________________________________________ 4 1.4 Culture-independent microbiology __________________________________________________________ 6 1.5 The bacterial ribosome and 16S rRNA _____________________________________________________ 10 1.6 The human microbiome ________________________________________________________________ 12 1.7 Microbial ecology _____________________________________________________________________ 13 1.8 Microbial biofilms ______________________________________________________________________ 14 1.9 Polymicrobial infections _________________________________________________________________ 16 1.10 The respiratory tract __________________________________________________________________ 18 1.10.1 Chronic respiratory tract diseases _____________________________________________________ 19 1.10.2 Respiratory tract defence mechanisms _________________________________________________ 21 1.11 Aims and objectives of research undertaken________________________________________________ 24 Chapter Two: Materials & methods ___________________________________________________________ 25 2.1 DNA polymerase enzymes and microbial diversity ____________________________________________ 25 2.1.1 Sandy soil sampling strategy __________________________________________________________ 25 2.1.2 DNA extraction from sandy soil ________________________________________________________
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