A population study of the upper airway microbiota in Busselton, Western Australia

• Main Author: Turek, Elena Miroslavovna
• Other Authors: Moffatt, Miriam ; Cookson, William ; Cox, Michael
• Published: Imperial College London 2018
• Subjects: 610
• Online Access: https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.762163

That the healthy lungs are sterile has been a subject of much debate. Recent studies employing culture independent techniques have focused on investigating the diseased lungs with little still being done to characterise the bacteria which sustain the healthy lung ecosystem. The Busselton Health Study (BHS) is a long running epidemiological study that focuses on defining and characterizing common diseases. Recently addition of oropharyngeal (throat) swabs to the BHS sample collection has occurred. The main aims of this thesis therefore were to assess the upper airway microbiome in healthy individuals and evaluate the changes to the bacterial composition under disease and environmental stress (smoking). A random population sample of 529 participants was studied consisting of 60 current-smokers, 216 ex-smokers and 253 never-smokers, out of which there were 77 asthmatics, 46 subjects with gastro-esophageal reflux disease (GERD), 19 patients with diabetes and 387 healthy individuals. Bacterial DNA was extracted from all swabs and 16S rRNA gene qPCR and next generation sequencing performed. The results indicated that airways of healthy individuals contain a diverse collection of bacteria. Through application of weighted correlation network analysis (WCNA), these bacteria were seen to work together in tight networks. As the BHS cohort is a general population sample no severe disease phenotypes were noted, hence limited changes in bacterial community structure of participants with disease compared to healthy participants were seen. Smoke exposure however had a profound effect on the microbiome, with current-smokers exhibiting a significant drop in bacterial burden, diversity and a change in community structure. There was depletion of Haemophillus spp. and Neisseria spp. in current-smokers, and a strong positive relationship with streptococci. Notably within the first few years after cessation of smoking the bacterial community of the airways appears to regenerate with an increase in community diversity. A streptococci specific quantification assay and sequencing method (based on the map gene) was established in order to dissect further the relationship at the species level of the genus Streptococcus with current-smoking. This identified an increased dominance of Streptococcus salivarius (an opportunistic pathogen) in current-smokers. In conclusion, a healthy airway microbiome contains a rich community of microorganisms. This is significantly impacted by smoking, leading to loss of diversity and a community dominated by streptococci. Diversity however can be restored if smoking cessation occurs.