Chronic obstructive pulmonary disease upper airway microbiota alpha diversity is associated with exacerbation phenotype: A case-control observational study

Alexa A. Pragman, Katherine A. Knutson, Trevor J. Gould, Richard E. Isaacson, Cavan S Reilly, Christine H Wendt

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


BACKGROUND: Chronic obstructive pulmonary disease (COPD) frequent exacerbators (FE) suffer increased morbidity and mortality compared to infrequent exacerbators (IE). The association between the oral and sputum microbiota and exacerbation phenotype is not well defined. The objective of this study was to determine key features that differentiate the oral and sputum microbiota of FEs from the microbiota of IEs during periods of clinical stability.

METHODS: We recruited 11 FE and 11 IE who had not used antibiotics or systemic corticosteroids in the last 1 month. Subjects provided oral wash and sputum samples, which underwent 16S V4 MiSeq sequencing and qPCR of 16S rRNA. Data were analyzed using Dada2 and R.

RESULTS: FE and IE were similar in terms of age, FEV 1 percent predicted (FEV1pp), pack-years of tobacco exposure, and St. George's Respiratory Questionnaire score. 16S copy numbers were significantly greater in sputum vs. oral wash (p = 0.01), but phenotype was not associated with copy number. Shannon diversity was significantly greater in oral samples compared to sputum (p = 0.001), and IE samples were more diverse than FE samples (p < 0.001). Sputum samples from FE had more Haemophilus and Moraxella compared to IE sputum samples, due to dominance of these COPD-associated taxa in three FE sputum samples. Amplicon sequencing variant (ASV)-level analysis of sputum samples revealed one ASV (Actinomyces) was significantly more abundant in IE vs. FE sputum (p adj  = 0.048, Wilcoxon rank-sum test), and this persisted after controlling for FEV1pp. Principal coordinate analysis using Bray-Curtis distance with PERMANOVA analyses demonstrated clustering by anatomic site, phenotype, inhaled corticosteroid use, current tobacco use, COPD severity, and last professional dental cleaning.

CONCLUSIONS: FE have less diverse oral and sputum microbiota than IE. Actinomyces was significantly more abundant in IE sputum than FE sputum. The oral and sputum microbiota of COPD subjects cluster based on multiple clinical factors, including exacerbation phenotype. Even during periods of clinical stability, the frequent exacerbator phenotype is associated with decreased alpha diversity, beta-diversity clustering, and changes in taxonomic abundance.

Original languageEnglish (US)
Article number114
JournalRespiratory research
Issue number1
StatePublished - Jun 7 2019

Bibliographical note

Funding Information:
This work was supported in part by a Career Development Award 1IK2CX001095 (A.A.P.) from the United states (U.S.) Department of Veterans Affairs Clinical Sciences Research and Development Service; 5KL2TR113 and the NIH Clinical and Translational Science Award at the University of Minnesota, 8UL1TR000114 (A.A.P.); and NIAID/NIH 5T32AI055433 (A.A.P). The study sponsors did not play a role in the study design; in the collection, analysis, or interpretation of data; in the writing of the report; or in the decision to submit the paper for publication. The corresponding author confirms that she had full access to all the data in the study and had final responsibility for the decision to submit for publication.

Publisher Copyright:
© 2019 The Author(s).


  • Haemophilus
  • Microbiota
  • Moraxella
  • Phenotype
  • Pulmonary disease, chronic obstructive
  • RNA, ribosomal, 16S
  • Sputum
  • Streptococcus
  • Pulmonary Disease, Chronic Obstructive/genetics
  • Prospective Studies
  • Moraxella/genetics
  • Humans
  • Middle Aged
  • Male
  • Case-Control Studies
  • Sputum/microbiology
  • Female
  • Aged
  • Lung/microbiology
  • Haemophilus/genetics
  • Microbiota/physiology

PubMed: MeSH publication types

  • Observational Study
  • Journal Article


Dive into the research topics of 'Chronic obstructive pulmonary disease upper airway microbiota alpha diversity is associated with exacerbation phenotype: A case-control observational study'. Together they form a unique fingerprint.

Cite this