Analysis of the lung microbiome in the "healthy" smoker and in COPD

PLoS ONE

Volumn 6, Issue 2, 2011, Pages

  Erb Downward, John R ^a   Thompson, Deborah L ^a   Han, Meilan K ^a   Freeman, Christine M ^a,b   McCloskey, Lisa ^a,b   Schmidt, Lindsay A ^a   Young, Vincent B ^a   Toews, Galen B ^a,b   Curtis, Jeffrey L ^a,b   Sundaram, Baskaran ^a   Martinez, Fernando J ^a   Huffnagle, Gary B ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b VA ANN ARBOR HEALTHCARE SYSTEM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA ADRENERGIC RECEPTOR STIMULATING AGENT; CORTICOSTEROID; BACTERIAL DNA; RNA 16S;

ADULT; AGED; AMPLICON; ARTICLE; BACTERIUM IDENTIFICATION; CHRONIC OBSTRUCTIVE LUNG DISEASE; CLINICAL ARTICLE; CONTROLLED STUDY; DISEASE SEVERITY; FEMALE; FUSOBACTERIUM; HAEMOPHILUS; HUMAN; HUMAN TISSUE; LUNG LAVAGE; LUNG PARENCHYMA; MALE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIOME; NONHUMAN; PORPHYROMONAS; PREVOTELLA; PSEUDOMONAS; PYROSEQUENCING; SMOKING; SPIROMETRY; STREPTOCOCCUS; TAXONOMY; VEILLONELLA; BRONCHOSCOPY; CLINICAL TRIAL; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; HEALTH; LUNG; METAGENOME; MICROBIOLOGY; MIDDLE AGED; PATHOLOGY;

BACTERIA (MICROORGANISMS); FUSOBACTERIUM; HAEMOPHILUS; PORPHYROMONAS; PREVOTELLA; PSEUDOMONAS; STREPTOCOCCUS; VEILLONELLA;

ADULT; AGED; BRONCHOALVEOLAR LAVAGE FLUID; BRONCHOSCOPY; DNA, BACTERIAL; FEMALE; HEALTH; HUMANS; LUNG; MALE; METAGENOME; MIDDLE AGED; PULMONARY DISEASE, CHRONIC OBSTRUCTIVE; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SMOKING;

EID: 79952063902     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016384     Document Type: Article

References (38)

1. Murray CJ, Lopez AD, (1996) Evidence-based health policy-lessons from the Global Burden of Disease Study. Science 274: 740-743.
2. Lopez AD, Shibuya K, Rao C, Mathers CD, Hansell AL, et al. (2006) Chronic obstructive pulmonary disease: current burden and future projections. Eur Respir J 27: 397-412.
3. Barnes P, Drazen J, Rennard S, Thomsom N, (2008) Asthma and COPD: Basic Mechanisms and Clinical Management.
4. Salvi SS, Barnes PJ, (2009) Chronic obstructive pulmonary disease in non-smokers. Lancet 374: 733-743.
5. Fletcher C, (1978) Community Health. J Epidemiol 32: 282-288.
6. Papi A, Luppi F, Franco F, Fabbri LM, (2006) Pathophysiology of exacerbations of chronic obstructive pulmonary disease. Proc Am Thorac Soc 3: 245-251.
7. Martinez FJ, Han MK, Flaherty K, Curtis J, (2006) Role of infection and antimicrobial therapy in acute exacerbations of chronic obstructive pulmonary disease. Expert Rev Anti Infect Ther 4: 101-124.
8. Baughman RP, Thorpe JE, Staneck J, Rashkin M, Frame PT, (1987) Use of the protected specimen brush in patients with endotracheal or tracheostomy tubes. Chest 91: 233-236.
9. Kahn FW, Jones JM, (1987) Diagnosing bacterial respiratory infection by bronchoalveolar lavage. J Infect Dis 155: 862-869.
10. Thorpe JE, Baughman RP, Frame PT, Wesseler TA, Staneck JL, (1987) Bronchoalveolar lavage for diagnosing acute bacterial pneumonia. J Infect Dis 155: 855-861.
11. Harris JK, De Groote MA, Sagel SD, Zemanick ET, Kapsner R, et al. (2007) Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Proc Natl Acad Sci U S A 104: 20529-20533.
12. Hilty M, Burke C, Pedro H, Cardenas P, Bush A, et al. (2010) Disordered microbial communities in asthmatic airways. PLoS One 5: e8578.
13. Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, et al. (2010) A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. OMICS 14: 9-59.
14. Rogers GB, Carroll MP, Serisier DJ, Hockey PM, Jones G, et al. (2004) characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16 s ribosomal DNA terminal restriction fragment length polymorphism profiling. J Clin Microbiol 42: 5176-5183.
15. Armougom F, Bittar F, Stremler N, Rolain JM, Robert C, et al. (2009) Microbial diversity in the sputum of a cystic fibrosis patient studied with 16S rDNA pyrosequencing. Eur J Clin Microbiol Infect Dis 28: 1151-1154.
16. Hankinson JL, Odencrantz JR, Fedan KB, (1999) Spirometric reference values from a sample of the general U.S. population. Am J Respir Crit Care Med 159: 179-187.
17. Marion MS, Leonardson GR, Rhoades ER, Welty TK, Enright PL, (2001) Spirometry reference values for American Indian adults: results from the Strong Heart Study. Chest 120: 489-495.
18. Rabe KF, Hurd S, Anzueto A, Barnes PJ, Buist SA, et al. (2007) Global strategy for the diagnosis, management, and prevention of chronic obstructive pulmonary disease: GOLD executive summary. Am J Respir Crit Care Med 176: 532-555.
19. Hattotuwa K, Gamble EA, O'Shaughnessy T, Jeffery PK, Barnes NC, (2002) Safety of bronchoscopy, biopsy, and BAL in research patients with COPD. Chest 122: 1909-1912.
20. Dowd SE, Callaway TR, Wolcott RD, Sun Y, McKeehan T, et al. (2008) Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMCMicrobiol 8: 125.
21. Bailey MT, Dowd SE, Parry NM, Galley JD, Schauer DB, et al. (2010) Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium. InfectImmun 78: 1509-1519.
22. Liu Z, DeSantis TZ, Andersen GL, Knight R, (2008) Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res 36: e120.
23. Oksanen Jari, Guillaume Blanchet F, Kindt Roeland, Legendre Pierre, O'Hara RB, et al. (2010) vegan: Community Ecology Package. R package version 1.17-3. 1.17-3 ed.
24. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
25. Wang Q, Garrity GM, Tiedje JM, Cole JR, (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
26. Lemon KP, Klepac-Ceraj V, Schiffer Hk, Brodie EL, Lynch SV, et al. (2010) Comparative Analyses of the Bacterial Microbiota of the Human Nostril and Oropharynx. mBio 1: 1-9.
27. Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, et al. (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 102: 11070-11075.
28. Schloss PD, Handelsman J, (2004) Status of the microbial census. Microbiol Mol Biol Rev 68: 686-691.
29. Bray J, Curtis J, (1957) An Ordination of the Upland Forest Communities of Southern Wisconsin. Ecological Monographs 27: 326-349.
30. Ott SJ, Musfeldt M, Wenderoth DF, Hampe J, Brant O, et al. (2004) Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 53: 685-693.
31. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, et al. (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 104: 13780-13785.
32. Curtis J, Freeman C, J. H, (2007) The immunopathology of chronic obstructive pulmonary disease. Insights from recent research. Proceedings of the American Thoracic 4: 412-421.
33. Sartor RB, (2008) Therapeutic correction of bacterial dysbiosis discovered by molecular techniques. Proc Natl Acad Sci U S A 105: 16413-16414.
34. Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, et al. (2006) Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55: 205-211.
35. Martinez FD, (1999) Role of respiratory infection in onset of asthma and chronic obstructive pulmonary disease. Clin Exp Allergy 29 (Suppl 2): 53-58.
36. Murphy TF, (2009) Pseudomonas aeruginosa in adults with chronic obstructive pulmonary disease. Curr Opin Pulm Med 15: 138-142.
37. Grice EA, Kong HH, Conlan S, Deming CB, Davis J, et al. (2009) Topographical and temporal diversity of the human skin microbiome. Science 324: 1190-1192.
38. Lepp PW, Brinig MM, Ouverney CC, Palm K, Armitage GC, et al. (2004) Methanogenic Archaea and human periodontal disease. Proc Natl Acad Sci U S A 101: 6176-6181.