16S rRNA gene sequencing reveals site-specific signatures of the upper and lower airways of cystic fibrosis patients

Sarah K. Lucas, Robert Yang, Jordan M Dunitz, Holly C Boyer, Ryan C Hunter

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

Abstract

Background: Metastasis of upper airway microbiota may have significant implications in the development of chronic lung disease. Here, we compare bacterial communities of matched sinus and lung mucus samples from cystic fibrosis (CF) subjects undergoing endoscopic surgery for treatment of chronic sinusitis. Methods: Mucus from one maxillary sinus and expectorated sputum were collected from twelve patients. 16S rRNA gene sequencing was then performed on sample pairs to compare the structure and function of CF airway microbiota. Results: Bacterial diversity was comparable between airway sites, though sinuses harbored a higher prevalence of dominant microorganisms. Ordination analyses revealed that samples clustered more consistently by airway niche rather than by individual. Finally, predicted metagenomes suggested that anaerobiosis was enriched in the lung. Conclusions: Our findings indicate that while the lung may be seeded by individual sinus pathogens, airway microenvironments harbor distinct bacterial communities that should be considered in selecting antimicrobial therapies.

Original languageEnglish (US)
Pages (from-to)204-212
Number of pages9
JournalJournal of Cystic Fibrosis
Volume17
Issue number2
DOIs
StatePublished - Mar 2018

Bibliographical note

Funding Information:
This work was supported by a Pathway to Independence Award from the National Heart Lung and Blood Institute to RCH ( R00HL114862 ); an Investigator-Sponsored Research Grant from Gilead Sciences to RCH, JD, and HCB; a Lions 5M International award to RY; a National Institutes of Health T32 Fellowship (# T90 DE 0227232 ) awarded through the National Institute of Dental and Craniofacial Research to SKL; and the University of Minnesota Medical School. We acknowledge the Minnesota Supercomputing Institute (MSI), Daryl Gohl and John Garbe at the UMN Genomics Center for sequencing assistance. We thank Abayo Itabiyi, Ali Stockness and Rebecca Dove of the Department of Otolaryngology, and the members of BioNet at the University of Minnesota for facilitating sample collection. Our thanks go out to Tonya Ward, Dan Knights, and the Knights Lab at UMN for their assistance with the BugBase analysis.

Funding Information:
This work was supported by a Pathway to Independence Award from the National Heart Lung and Blood Institute to RCH (R00HL114862); an Investigator-Sponsored Research Grant from Gilead Sciences to RCH, JD, and HCB; a Lions 5M International award to RY; a National Institutes of Health T32 Fellowship (#T90 DE 0227232) awarded through the National Institute of Dental and Craniofacial Research to SKL; and the University of Minnesota Medical School. We acknowledge the Minnesota Supercomputing Institute (MSI), Daryl Gohl and John Garbe at the UMN Genomics Center for sequencing assistance. We thank Abayo Itabiyi, Ali Stockness and Rebecca Dove of the Department of Otolaryngology, and the members of BioNet at the University of Minnesota for facilitating sample collection. Our thanks go out to Tonya Ward, Dan Knights, and the Knights Lab at UMN for their assistance with the BugBase analysis.

Keywords

  • Chronic sinusitis
  • Microbial ecology
  • Microbiome
  • Mucus

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