Our initial study, funded by the Channel 7 Children’s Research Foundation, investigated the microbiota associated with the upper and lower respiratory tract in 35 children with chronic suppurative lung disease, 10 children with protracted bacterial bronchitis and 10 children without respiratory illness. The CRE funding enabled us to extend that study by including an additional 20 children with protracted bacterial bronchitis. The two studies undertook 16S rRNA gene sequencing of nasopharyngeal swabs, throat swabs and bronchoalveolar lavage (fluid wash of the lungs) to identify the microbes present. Data from the studies were analysed jointly to maximise the outcomes of both studies.


Our results indicated that the diversity of the microbiota present in the nasopharyngeal swabs showed an upward trend associated with disease severity, with significantly higher bacterial diversity found in children with chronic suppurative lung compared with healthy controls. We also undertook comparative analysis of upper (nasopharyngeal swabs) and lower airway (bronchoalveolar lavage) microbiota to assess the usefulness of upper airway sampling, which is much less invasive, as a surrogate measure of lower airway microbiota. The findings are important to understanding the strengths and limitations of using upper airway sampling in longitudinal studies of chronic lung disease in children who don’t expectorate. We found that while upper airway sampling provided an imperfect measure of lower airway microbiota, the data did provide a meaningful measure that could be used to infer differences between clinically-defined groups. Initial analysis of the relationships between the microbiota and inflammatory markers showed that the immune markers IL-1β and IL-8 were positively correlated with the percentage of neutrophils (type of white blood cells) and the amount of bacteria present in the lungs.

The data generated by this study have been used in several ways to provide new knowledge about the airway microbiota in young children with chronic lung disease. We have detected differences in the bacterial community structure in airway specimens from children in each diagnostic group, with some samples dominated by a small number of taxa at high relative abundance and others having a more even distribution. This suggests overgrowth by single species in some children. We are investigating this observation further to understand relationships between the dominant taxa and clinical markers of inflammation and disease severity. We are now extending our studies to include samples from native Alaskan children as a part of an exchange visit between two CRE sites- Dr Robyn Marsh from the Menzies School of Health Research in Darwin spent 2016 in the laboratory of Professor Luke Hoffman at the University of Washington in Seattle.

Main publications:

Chest. 2019 Apr;155(4):778-786  https://www.ncbi.nlm.nih.gov/pubmed/30660785

Microbiome. 2016 Jul 7;4(1):37  https://www.ncbi.nlm.nih.gov/pubmed/27388563

Lead investigator
Dr Robyn Marsh
Chief investigator
Professor John Upham and Professor Anne Chang
Project period