Analysis of the Airway Microbiota of Healthy Individuals and Patients with Chronic Obstructive Pulmonary Disease by T-RFLP and Clone Sequencing

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2013 Jul 23

PMID 23874580

Citations 53

Authors

Tetyana Zakharkina

Elke Heinzel

Rembert A Koczulla

Timm Greulich

Katharina Rentz

Josch K Pauling

Jan Baumbach

Mathias Herrmann

Christiane Grunewald

Hendrik Dienemann

Lutz von Muller

Robert Bals

Affiliations

Soon will be listed here.

Abstract

Unlabelled: Chronic obstructive pulmonary disease (COPD) is a progressive, inflammatory lung disease that affects a large number of patients and has significant impact. One hallmark of the disease is the presence of bacteria in the lower airways.

Objective: The aim of this study was to analyze the detailed structure of microbial communities found in the lungs of healthy individuals and patients with COPD. Nine COPD patients as compared and 9 healthy individuals underwent flexible bronchoscopy and BAL was performed. Bacterial nucleic acids were subjected to terminal restriction fragment (TRF) length polymorphism and clone library analysis. Overall, we identified 326 T-RFLP band, 159 in patients and 167 in healthy controls. The results of the TRF analysis correlated partly with the data obtained from clone sequencing. Although the results of the sequencing showed high diversity, the genera Prevotella, Sphingomonas, Pseudomonas, Acinetobacter, Fusobacterium, Megasphaera, Veillonella, Staphylococcus, and Streptococcus constituted the major part of the core microbiome found in both groups. A TRF band possibly representing Pseudomonas sp. monoinfection was associated with a reduction of the microbial diversity. Non-cultural methods reveal the complexity of the pulmonary microbiome in healthy individuals and in patients with COPD. Alterations of the microbiome in pulmonary diseases are correlated with disease.

Citing Articles

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References

Erb-Downward J, Thompson D, Han M, Freeman C, McCloskey L, Schmidt L . Analysis of the lung microbiome in the "healthy" smoker and in COPD. PLoS One. 2011; 6(2):e16384. PMC: 3043049. DOI: 10.1371/journal.pone.0016384. View

Zakharkina T, Koczulla A, Mardanova O, Hattesohl A, Bals R . Detection of microorganisms in exhaled breath condensate during acute exacerbations of COPD. Respirology. 2011; 16(6):932-8. DOI: 10.1111/j.1440-1843.2011.01977.x. View

Proctor L . The Human Microbiome Project in 2011 and beyond. Cell Host Microbe. 2011; 10(4):287-91. DOI: 10.1016/j.chom.2011.10.001. View

Joliffe I, Morgan B . Principal component analysis and exploratory factor analysis. Stat Methods Med Res. 1992; 1(1):69-95. DOI: 10.1177/096228029200100105. View

Sibley C, Parkins M, Rabin H, Surette M . The relevance of the polymicrobial nature of airway infection in the acute and chronic management of patients with cystic fibrosis. Curr Opin Investig Drugs. 2009; 10(8):787-94. View

Sibley C, Surette M . The polymicrobial nature of airway infections in cystic fibrosis: Cangene Gold Medal Lecture. Can J Microbiol. 2011; 57(2):69-77. DOI: 10.1139/w10-105. View

Pauly J, Paszkiewicz G . Cigarette smoke, bacteria, mold, microbial toxins, and chronic lung inflammation. J Oncol. 2011; 2011:819129. PMC: 3136185. DOI: 10.1155/2011/819129. View

Heijink I, Brandenburg S, Postma D, van Oosterhout A . Cigarette smoke impairs airway epithelial barrier function and cell-cell contact recovery. Eur Respir J. 2011; 39(2):419-28. DOI: 10.1183/09031936.00193810. View

Lemon K, Klepac-Ceraj V, Schiffer H, Brodie E, Lynch S, Kolter R . Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. mBio. 2010; 1(3). PMC: 2925076. DOI: 10.1128/mBio.00129-10. View

10.

GABRIEL K, Odoroff C . Biplots in biomedical research. Stat Med. 1990; 9(5):469-85. DOI: 10.1002/sim.4780090502. View

11.

Collins M, Wallbanks S, Lane D, Shah J, Nietupski R, Smida J . Phylogenetic analysis of the genus Listeria based on reverse transcriptase sequencing of 16S rRNA. Int J Syst Bacteriol. 1991; 41(2):240-6. DOI: 10.1099/00207713-41-2-240. View

12.

Lee Z, Bussema 3rd C, Schmidt T . rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res. 2008; 37(Database issue):D489-93. PMC: 2686494. DOI: 10.1093/nar/gkn689. View

13.

Brown C, Wong M, Davis C, Kanti A, Zhou X, Forney L . Preliminary characterization of the normal microbiota of the human vulva using cultivation-independent methods. J Med Microbiol. 2007; 56(Pt 2):271-276. DOI: 10.1099/jmm.0.46607-0. View

14.

Sethi S . Infection as a comorbidity of COPD. Eur Respir J. 2010; 35(6):1209-15. DOI: 10.1183/09031936.00081409. View

15.

Schloss P, Handelsman J . Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 2005; 71(3):1501-6. PMC: 1065144. DOI: 10.1128/AEM.71.3.1501-1506.2005. View

16.

OToole P . Changes in the intestinal microbiota from adulthood through to old age. Clin Microbiol Infect. 2012; 18 Suppl 4:44-6. DOI: 10.1111/j.1469-0691.2012.03867.x. View

17.

Huang Y, Kim E, Cox M, Brodie E, Brown R, Wiener-Kronish J . A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. OMICS. 2010; 14(1):9-59. PMC: 3116451. DOI: 10.1089/omi.2009.0100. View

18.

Liu Z, Zhang W, Zhang J, Zhou X, Zhang L, Song Y . Oral hygiene, periodontal health and chronic obstructive pulmonary disease exacerbations. J Clin Periodontol. 2011; 39(1):45-52. DOI: 10.1111/j.1600-051X.2011.01808.x. View

19.

Markowitz V, Chen I, Chu K, Szeto E, Palaniappan K, Grechkin Y . IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 2011; 40(Database issue):D123-9. PMC: 3245048. DOI: 10.1093/nar/gkr975. View

20.

Diederen B, van der Valk P, Kluytmans J, Peeters M, Hendrix R . The role of atypical respiratory pathogens in exacerbations of chronic obstructive pulmonary disease. Eur Respir J. 2007; 30(2):240-4. DOI: 10.1183/09031936.00012707. View