title: A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation.
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.
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, USA.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Quinn
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, USA.
authors.forename: Katrine
authors.initials: K
authors.lastname: Whiteson
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, USA.
authors.forename: Yan-Wei
authors.initials: YW
authors.lastname: Lim
authors.affiliation: Department of Mathematics and Statistics, San Diego State University, San Diego, CA, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Salamon
authors.affiliation: Department of Mathematics and Statistics, San Diego State University, San Diego, CA, USA.
authors.forename: Barbara
authors.initials: B
authors.lastname: Bailey
authors.affiliation: Department of Chemistry, University of California, Irvine, CA, USA.
authors.forename: Simone
authors.initials: S
authors.lastname: Mienardi
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, USA.
authors.forename: Savannah E
authors.initials: SE
authors.lastname: Sanchez
authors.affiliation: Department of Chemistry, University of California, Irvine, CA, USA.
authors.forename: Don
authors.initials: D
authors.lastname: Blake
authors.affiliation: Department of Medicine, University of California, San Diego, CA, USA.
authors.forename: Doug
authors.initials: D
authors.lastname: Conrad
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA, USA.
authors.forename: Forest
authors.initials: F
authors.lastname: Rohwer
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D001421:Bacteria, Anaerobic / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D001431:Bacteriological Techniques; D003550:Cystic Fibrosis / Q000382:microbiology*; D005285:Fermentation; D006801:Humans; D008168:Lung / Q000382:microbiology; D011550:Pseudomonas aeruginosa / Q000235:genetics; D013183:Sputum / Q000382:microbiology