ArticleProceedings of the National Academy of Sciences of the United States of America2012
Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 153 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
153 citing papers in PubMed, 256 citations in OpenAlex.
- Spatial Variation in the Healthy Human Lung Microbiome and the Adapted Island Model of Lung Biogeography.Annals of the American Thoracic Society · 2015Trial
- Iron supplementation does not worsen respiratory health or alter the sputum microbiome in cystic fibrosis.Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society · 2014Trial
- Characteristics of Respiratory Microbiome in COPD-A Literature Review.Advances in respiratory medicine · 2026Review
- The microbiome and gut-lung axis in nontuberculous mycobacterial pulmonary disease.PLoS pathogens · 2025Review
- Airway Microbiome in Children with Cystic Fibrosis: A Review of Microbial Shifts and Therapeutic Impacts.Medicina (Kaunas, Lithuania) · 2025Review
- The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease.European respiratory review : an official journal of the European Respiratory Society · 2025Review
- Direct assessment of airway microbiota in primary ciliary dyskinesia end-stage lung disease.ERJ open research · 2025Article
- Characteristics of upper and lower respiratory tract microbiota after lung transplantation.Respiratory research · 2025Article
- Review
- Positioning the preventive potential of microbiome treatments for cystic fibrosis in the context of current therapies.Cell reports. Medicine · 2024Review
- Effect of hyperglycemia on lung microbiota and treatment outcome in pulmonary tuberculosis: A scoping review.F1000Research · 2024Article
- Review
- Upper airway microbiota development in infants with cystic fibrosis diagnosed by newborn screen.Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society · 2023Article
- Genome-wide mapping of gene-microbe interactions in the murine lung microbiota based on quantitative microbial profiling.Animal microbiome · 2023Article
- Single nucleotide variants inMicrobial genomics · 2023Article
- Alteration of the Respiratory Microbiome in Hospitalized Patients with Asthma-COPD Overlap during and after an Exacerbation.Journal of clinical medicine · 2023Article
- Antibiotics Drive Expansion of Rare Pathogens in a Chronic Infection Microbiome Model.mSphere · 2022Article
- Microbiosis in lung allotransplantation and xenotransplantation: State of the art and future perspective.Health care science · 2022Review
- Exploring the Cystic Fibrosis Lung Microbiome: Making the Most of a Sticky Situation.Journal of the Pediatric Infectious Diseases Society · 2022Review
- Utilizing the Gastrointestinal Microbiota to Modulate Cattle Health through the Microbiome-Gut-Organ Axes.Microorganisms · 2022Review
93 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent work using culture-independent methods suggests that the lungs of cystic fibrosis (CF) patients harbor a vast array of bacteria not conventionally implicated in CF lung disease. However, sampling lung secretions in living subjects requires that expectorated specimens or collection devices pass through the oropharynx. Thus, contamination could confound results. Here, we compared culture-independent analyses of throat and sputum specimens to samples directly obtained from the lungs at the time of transplantation. We found that CF lungs with advanced disease contained relatively homogenous populations of typical CF pathogens. In contrast, upper-airway specimens from the same subjects contained higher levels of microbial diversity and organisms not typically considered CF pathogens. Furthermore, sputum exhibited day-to-day variation in the abundance of nontypical organisms, even in the absence of clinical changes. These findings suggest that oropharyngeal contamination could limit the accuracy of DNA-based measurements on upper-airway specimens. This work highlights the importance of sampling procedures for microbiome studies and suggests that methods that account for contamination are needed when DNA-based methods are used on clinical specimens.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.