Abstract
There is a poor understanding of how the physiology of polymicrobial communities in cystic fibrosis (CF) lungs contributes to pulmonary exacerbations and lung function decline. In this study, a microbial culture system based on the principles of the Winogradsky column (WinCF system) was developed to study the physiology of CF microbes. The system used glass capillary tubes filled with artificial sputum medium to mimic a clogged airway bronchiole. Chemical indicators were added to observe microbial physiology within the tubes. Characterization of sputum samples from seven patients showed variation in pH, respiration, biofilm formation and gas production, indicating that the physiology of CF microbial communities varied among patients. Incubation of homogenized tissues from an explant CF lung mirrored responses of a Pseudomonas aeruginosa pure culture, supporting evidence that end-stage lungs are dominated by this pathogen. Longitudinal sputum samples taken through two exacerbation events in a single patient showed that a two-unit drop in pH and a 30% increase in gas production occurred in the tubes prior to exacerbation, which was reversed with antibiotic treatment. Microbial community profiles obtained through amplification and sequencing of the 16S rRNA gene showed that fermentative anaerobes became more abundant during exacerbation and were then reduced during treatment where P. aeruginosa became the dominant bacterium. Results from the WinCF experiments support the model where two functionally different CF microbial communities exist, the persistent Climax Community and the acute Attack Community. Fermentative anaerobes are hypothesized to be the core members of the Attack Community and production of acidic and gaseous products from fermentation may drive developing exacerbations. Treatment targeting the Attack Community may better resolve exacerbations and resulting lung damage.
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Change history
17 March 2014
This article has been corrected since Advance Online Publication and a corrigendum is also printed in this issue
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Acknowledgements
This work was supported by the National Institute of Health through grant R01 GM095384-01 awarded to Forest Rohwer. The project was partially supported by the National Institutes of Health, grant UL1RR031980 for years 1 and 2 of CTSA funding and/or UL1TR000100 during year 3 and beyond of CTSA funding. Funding was also provided by the Canadian Institute for Advanced Research and by the Cystic Fibrosis Research Inc. Elizabeth Nash memorial fellowship awarded to Robert Quinn. We also thank Mark Hatay and Amadeo Candido for their contributions to the imaging set up and mucus_analyzer script development.
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Quinn, R., Whiteson, K., Lim, YW. et al. A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation. ISME J 9, 1024–1038 (2015). https://doi.org/10.1038/ismej.2014.234
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DOI: https://doi.org/10.1038/ismej.2014.234
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