The DOI matches its Crossref record; 34 of the 34 references it cites were found in a registry or an index.
Changes in Cystic Fibrosis Airway Microbiota at Pulmonary Exacerbation
Open accessAbstract
RATIONALE: In persons with cystic fibrosis (CF), repeated exacerbations of pulmonary symptoms are associated with a progressive decline in lung function. Changes in the airway microbiota around the time of exacerbations are not well understood. OBJECTIVES: To characterize changes in airway bacterial communities around the time of exacerbations and to identify predictors for these changes. METHODS: DNA prepared from 68 paired baseline and exacerbation sputum samples collected from 28 patients with CF were subjected to barcoded 16S rRNA gene pyrosequencing. Bacterial density was calculated by quantitative PCR. MEASUREMENTS AND MAIN RESULTS: Overall, significant differences in bacterial community diversity and bacterial density between baseline and exacerbation samples were not observed. However, considerable changes in community structures were observed in a subset of patients. In these patients, the dominant taxa and initial level of community diversity were significant predictors of the magnitude of community structure changes at exacerbation. Pseudomonas-dominant communities became more diverse at exacerbation compared with communities with other or no dominant species. The relative abundance of Gemella increased in 24 (83%) of 29 samples at exacerbation and was found to be the most discriminative genus between baseline and exacerbation samples. CONCLUSIONS: The magnitude of changes in the CF lung microbiota around the time of exacerbation was found to be largely dependent on community diversity and composition at baseline. Certain genera appear to play important roles in driving change in airway bacterial community composition at exacerbation. Gemella might play a direct role in and/or be a biomarker for pulmonary exacerbation.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“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 [136]
Citations
Cites
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 21,481
A new method for non-parametric multivariate analysis of variance
Anderson, M. J. (2001) · Austral Ecology · doi:10.1111/j.1442-9993.2001.01070.pp.x · Cited by 13,828
An Ordination of the Upland Forest Communities of Southern Wisconsin
Bray, J. R., & Curtis, J. T. (1957) · Ecological Monographs · doi:10.2307/1942268 · Cited by 11,736
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
Schloss, P. D., Gevers, D., & Westcott, S. L. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027310 · Cited by 2,112
Self-citationNadkarni, M. A., Martin, F. E., Jacques, N. A., & Hunter, N. (2002) · Microbiology · doi:10.1099/00221287-148-1-257 · Cited by 1,931
The keystone-pathogen hypothesis
Hajishengallis, G., Darveau, R. P., & Curtis, M. A. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2873 · Cited by 1,790
Hajishengallis, G., Liang, S., Payne, M. A., Hashim, A., Jotwani, R., Eskan, M. A., McIntosh, M. L., Alsam, A., Kirkwood, K. L., Lambris, J. D., et al. (2011) · Cell Host & Microbe · doi:10.1016/j.chom.2011.10.006 · Cited by 1,154
Nonparametric estimation of Shannon’s index of diversity when there are unseen species in sample
Chao, A., & Shen, T. (2003) · Environmental and Ecological Statistics · doi:10.1023/a:1026096204727 · Cited by 810
Predictive 5-year survivorship model of cystic fibrosis
Liou, T. G., Adler, F. R., FitzSimmons, S. C., Cahill, B. C., Hibbs, J. R., & Marshall, B. C. (2001) · American Journal of Epidemiology · doi:10.1093/aje/153.4.345 · Cited by 749
Decade-long bacterial community dynamics in cystic fibrosis airways
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., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120577109 · Cited by 599
Self-citation
Flagged first, then by citations
Research works printed but not linked: 1
- Liaw, 2002, Classification and regression by randomforest, R News, 2, 18
Cited by
Sorted by citations
Items 201–240 of 240
Exploring the human microbiome: Its role and impact on overall health and disease prevention
Alotaibi, F. M., Almazam, . A., Alenezi, S. Z., Alanazi, . H., Lamfon, . A., Albalawi, A. E. A., Al-Nasser, N. S., & Altheyab, S. A. (2018) · International Journal of Health Sciences · doi:10.53730/ijhs.v2ns1.15085 · Cited by 1
The Lung Microbiome and Its Impact on Obstructive Sleep Apnea: A Diagnostic Frontier
Karkala, A., Kotoulas, S., Tzinas, A., Massa, E., Mouloudi, E. K., Gkakou, F., & Pataka, A. (2025) · Diagnostics · doi:10.3390/diagnostics15111431 · Cited by 1
Somayaji, R., & Quon, B. S. (2023) · Current Opinion in Pulmonary Medicine · doi:10.1097/mcp.0000000000001010 · Cited by 1
Gonzales, G., Malka, R. E., Marinelli, L. M., Lee, C. M., Cook, S., Miar, S., Dion, G. R., & Guda, T. (2024) · Respiratory Research · doi:10.1186/s12931-024-02973-1 · Cited by 1
Rong, K., Kuang, H., Ou, L., Fang, R., Kuang, J., & Yang, H. (2024) · Discover Oncology · doi:10.1007/s12672-024-01247-y · Cited by 1
RetractedTesting the neutral theory of biodiversity with the microbiome dataset from cystic fibrosis patients
Huang, Q., Wang, Y., Yao, X. Y., Li, L., Luo, J., Xia, S., Sun, Y., Miao, Y., Wang, K., & Chen, Y. (2018) · Medicine · doi:10.1097/md.0000000000012248 · Cited by 1
Rogers, G. B., & Huang, Y. J. (2019) · European Respiratory Society eBooks · doi:10.1183/2312508x.10016218 · Cited by 1
Uluer, A., & Marty, F. M. (2015) · Elsevier eBooks · doi:10.1016/b978-1-4557-4801-3.00073-4 · Cited by 2
Verma, N., Thapa, K., & Dua, K. (2021) · Springer eBooks · doi:10.1007/978-981-33-6827-9_39 · Cited by 1
What to Expect When You’re Expectorating: Cystic Fibrosis Exacerbations and Microbiota
Hoffman, L. R., & Surette, M. G. (2013) · Annals of the American Thoracic Society · doi:10.1513/annalsats.201304-086ed · Cited by 1
Bacterial Diversity in Cases of Lung Infection in Cystic Fibrosis Patients
European Cystic Fibrosis Society Lung Microbiome Working Group (2014) · Springer eBooks · doi:10.1007/978-1-4614-6418-1_470-2 · Cited by 1
Mancini, L., Saliekh, L., Claydon, R., Kotar, J., Bényei, É. B., Munro, C. A., Shendruk, T. N., Brown, A. T., Welch, M., & Cicuta, P. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.22.644766 · Cited by 1
PULMONARY, SLEEP, AND CRITICAL CARE UPDATE Update in Cystic Fibrosis 2014
Ong, T., & Ramsey, B. W. (2015)
Modelos estocásticos de ecología de bacterias y virus
Delgado, R. Á. V. (2019) · doi:10.20868/upm.thesis.54318
The Pulmonary Microbiome in Cystic Fibrosis
Frost, F. J., Nazareth, D. S., & Wat, D. (2020) · IntechOpen eBooks · doi:10.5772/intechopen.91765
Morales, O., Rosero-Ascuntar, C. A., Cuellar, M., Aristizábal-Serna, E. A., & Villegas-Castaño, A. (2020) · Infectio · doi:10.22354/in.v24i4.881
Rogers, G. B. (2018) · European Respiratory Society eBooks · doi:10.1183/2312508x.10015617
Effects of Therapy on Host-Microbe Interactions in Pediatric Inflammatory Bowel Diseases
Dijk, S. (2020) · ERA: Education and Research Archive (University of Alberta) · doi:10.7939/r3-w5w4-2d33
Lucas, S. K. (2020) · University of Minnesota Digital Conservancy (University of Minnesota)
Lung Diseases: Chronic Respiratory Infections
Blasi, F. (2018) · MDPI eBooks · doi:10.3390/books978-3-03897-339-3
Quon, B. S. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.727579272.793545660
Bacterial Diversity in Cases of Lung Infection in Cystic Fibrosis Patients
European Cystic Fibrosis Society Lung Microbiome Working Group (2015) · Springer eBooks · doi:10.1007/978-1-4899-7475-4_470
The Microbiome in Critically Ill Patients
Tulli, G., & Zuanetti, G. (2022) · Springer eBooks · doi:10.1007/978-3-031-14612-1_7
Bystrova, S. G., Simonova, O. I., Kustova, O. V., Akhmedova, E. E., & Lazareva, A. (2023) · Russian Pediatric Journal · doi:10.46563/1560-9561-2023-26-1-14-21
Song, W. H. C., Wong, K., Goldfarb, D. A., Bone, J. N., & Rayment, J. H. (2023) · Journal of Cystic Fibrosis · doi:10.1016/j.jcf.2023.10.007
Additional file 1 of Microbiota and mycobiota in bronchoalveolar lavage fluid of silicosis patients
Xie, L., Zhang, X., Gao, X., Wang, L., Cheng, Y., Zhang, S., Ji, Y., Tang, Y., Deng, Y., Zhang, B., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23658132
Le microbiote pulmonaire, perspective d’innovation en microbiologie médicale
Héry-Arnaud, G. (2024) · Revue Francophone des Laboratoires · doi:10.1016/s1773-035x(24)76117-6
Research Progress on Interaction and Influence between Pneumoconiosis and Microorganisms
杨, 天. (2025) · Advances in Microbiology · doi:10.12677/amb.2025.141006
Structural and Functional Pulmonary MRI to Predict Pulmonary Exacerbations in Cystic Fibrosis
Matheson, A. M., Bdaiwi, A. S., Willmering, M. M., DiFrancesco, M. W., Cleveland, Z. I., Santyr, G. E., Ratjen, F. A., Kramer, E. L., Szczesniak, R. D., & Woods, J. C. (2025) · CHEST Journal · doi:10.1016/j.chest.2025.10.041
Gonzales, G., Malka, R. E., Marinelli, L. M., Lee, C. M., Cook, S., Miar, S., Dion, G. R., & Guda, T. (2024) · Figshare · doi:10.6084/m9.figshare.27129494
Avalos, M., Alin, T., Métayer, C., Thiébaut, R., Enaud, R., & Delhaès, L. (2022) · Figshare · doi:10.6084/m9.figshare.20580927
Additional file 1 of Azithromycin and the microbiota of cystic fibrosis sputum
Acosta, N., Thornton, C. S., Surette, M. G., Somayaji, R., Rossi, L., Rabin, H. R., & Parkins, M. D. (2021) · Figshare · doi:10.6084/m9.figshare.14344114
Density fluctuations of Burkholderia and Achromobacter in cystic fibrosis sputum
Carmody, L. A., Caverly, L. J., Kalikin, L. M., Thornton, C. S., Simon, R. H., VanDevanter, D. R., & LiPuma, J. J. (2026) · Journal of Cystic Fibrosis · doi:10.1016/j.jcf.2026.03.006
Pagès, L. (2016) · theses.fr (ABES) · doi:10.70675/9d450abbzb581z49cez9268z17379d9c31b5
Volpato, F. C. Z., Lovison, O. V. A., de Lima-Morales, D., Almeida, É. K., Rampelotto, P. H., Martins, A. F., Maróstica, P. J. C., & Barth, A. L. (2026) · The Brazilian Journal of Infectious Diseases · doi:10.1016/j.bjid.2026.105876
Parolin, C., Gentile, E., Pellegrino, C., Spada, V., Bassi, C., Sabbioni, S., Vitali, B., Pinton, P., & Rimessi, A. (2026) · Biomedicines · doi:10.3390/biomedicines14091965
Madsen, K., Lolle, S., Bojer, M. S., Ingmer, H., Johansen, H. K., Molin, S., & Rosa, R. L. (2026) · ISME Communications · doi:10.1093/ismeco/ycag284
Metadata
- Authors
- Carmody, L. A., Zhao, J., Schloss, P. D., Petrosino, J. F., Murray, S., Young, V. B., Li, J. Z., & LiPuma, J. J.
- Affiliations
- University of Michigan (US)
- Microbiology and Immunology
- Baylor College of Medicine (US)
- Departments of Pediatrics and Communicable Disease and
- Corresponding author
- LiPuma, John J.
- ORCID
- Venue
- Annals of the American Thoracic Society
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-06-01
- Volume
- 10
- Issue
- 3
- Pages
- 179-187
- ISSN
- 2325-6621 (ISSN-L)
- 2329-6933
- PMC
- PMC3960905
- OpenAlex
- W2129800212
- Cited by
- 239
- References
- 34
- Citations by year
- 2026: 4 · 2025: 10 · 2024: 12 · 2023: 19 · 2022: 19 · 2021: 19 · 2020: 23 · 2019: 22 · 2018: 18 · 2017: 28 · 2016: 17 · 2015: 30 · 2014: 15 · 2013: 3
- FWCI
- 17.61
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Annals of the American Thoracic Society (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Cystic Fibrosis Foundation
- Georgia Clinical and Translational Science Alliance
- 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)
- 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
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Chronic Obstructive Pulmonary Disease (COPD) Research
- Keywords
- cystic fibrosis, pulmonary exacerbations, airway microbiome, bacterial community diversity, community composition, Pseudomonas, Gemella, biomarkers, lung function decline
- MeSH terms
- Adolescent, Adult, Child, Cystic Fibrosis, Female, Humans, Lung, Male, Middle Aged, Sputum, Disease Progression, Young Adult, Microbiota
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
