Decade-long bacterial community dynamics in cystic fibrosis airways
Open accessAbstract
The structure and dynamics of bacterial communities in the airways of persons with cystic fibrosis (CF) remain largely unknown. We characterized the bacterial communities in 126 sputum samples representing serial collections spanning 8-9 y from six age-matched male CF patients. Sputum DNA was analyzed by bar-coded pyrosequencing of the V3-V5 hypervariable region of the 16S rRNA gene, defining 662 operational taxonomic units (OTUs) from >633,000 sequences. Bacterial community diversity decreased significantly over time in patients with typically progressive lung disease but remained relatively stable in patients with a mild lung disease phenotype. Antibiotic use, rather than patient age or lung function, was the primary driver of decreasing diversity. Interpatient variability in community structure exceeded intrapatient variability in serial samples. Antibiotic treatment was associated with pronounced shifts in community structure, but communities showed both short- and long-term resilience after antibiotic perturbation. There was a positive correlation between OTU occurrence and relative abundance, with a small number of persistent OTUs accounting for the greatest abundance. Significant changes in community structure, diversity, or total bacterial density at the time of pulmonary exacerbation were not observed. Despite decreasing community diversity in patients with progressive disease, total bacterial density remained relatively stable over time. These findings show the critical relationship between airway bacterial community structure, disease stage, and clinical state at the time of sample collection. These features are the key parameters with which to assess the complex ecology of the CF airway.
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Culture-independent studies comparing bacterial communities at baseline and during exacerbations in the airways of patients with COPD, cystic fibrosis, or bronchiectasis consistently report no increase in bacterial burden and no decrease in community diversity during exacerbations.
“With remarkable consistency, all studies report no increase in bacterial burden and no decrease in community diversity during exacerbations.”
From The microbiome and critical illness (2016) · cites this paper as [135]
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- Authors
- Zhao, J., Schloss, P. D., Kalikin, L. M., Carmody, L. A., Foster, B. K., Petrosino, J. F., Cavalcoli, J. D., VanDevanter, D. R., Murray, S., Li, J. Z., Young, V. B., & LiPuma, J. J.
- Affiliations
- University of Michigan (US)
- Microbiology and Immunology,
- Baylor College of Medicine (US)
- Case Western Reserve University (US)
- Biostatistics and
- Human Genetics, and
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2012-03-26
- Volume
- 109
- Issue
- 15
- Pages
- 5809-5814
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3326496
- OpenAlex
- W2094167812
- Cited by
- 599
- References
- 18
- Citations by year
- 2026: 12 · 2025: 18 · 2024: 32 · 2023: 31 · 2022: 37 · 2021: 41 · 2020: 57 · 2019: 57 · 2018: 40 · 2017: 39 · 2016: 50 · 2015: 61 · 2014: 63 · 2013: 43 · 2012: 18
- FWCI
- 47.73
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Deep Blue (University of Michigan) (submittedVersion)
- Funders
- National Institutes of Health (5rc1hl100809-02)
- National Heart, Lung, and Blood Institute (U01HL098961, RC1-HL100809, 1RC1HL100809-01)
- National Human Genome Research Institute (R01HG005975, R01HG004906)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30DK034933, P30DK027651)
- National Center for Research Resources (UL1RR024986)
- Topics
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Cystic Fibrosis Research Advances
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bacterial biofilms and quorum sensing
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- cystic fibrosis, sputum microbiome, bacterial diversity, antibiotic therapy, community resilience, pulmonary exacerbations, disease progression, 16S rRNA gene sequencing, interpatient variability
- MeSH terms
- Adolescent, Adult, Aging, Anti-Bacterial Agents, Bacteria, Cystic Fibrosis, Humans, Lung, Male, Respiratory Function Tests, Sputum, Disease Progression, Principal Component Analysis, Biodiversity, Metagenome, Young Adult, Bacterial Load
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