Ivanov II, Frutos Rde L, Manel N, Yoshinaga K, Rifkin DB, Sartor RB, Finlay BB, Littman DR: Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe. 2008, 4: 337-349. 10.1016/j.chom.2008.09.009.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chung H, Pamp SJ, Hill JA, Surana NK, Edelman SM, Troy EB, Reading NC, Villablanca EJ, Wang S, Mora JR, Umesaki Y, Mathis D, Benoist C, Relman DA, Kasper DL: Gut immune maturation depends on colonization with a host-specific microbiota. Cell. 2012, 149: 1578-1593. 10.1016/j.cell.2012.04.037.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rogers GB, Daniels TW, Tuck A, Carroll MP, Connett GJ, David GJ, Bruce KD: Studying bacteria in respiratory specimens by using conventional and molecular microbiological approaches. BMC Pulm Med. 2009, 9: 14-10.1186/1471-2466-9-14.
Article
PubMed Central
PubMed
Google Scholar
Cabello H, Torres A, Celis R, El-Ebiary M, Puig de la Bellacasa J, Xaubet A, Gonzalez J, Agusti C, Soler N: Bacterial colonization of distal airways in healthy subjects and chronic lung disease: a bronchoscopic study. Eur Respir J. 1997, 10: 1137-1144. 10.1183/09031936.97.10051137.
Article
CAS
PubMed
Google Scholar
Charlson ES, Bittinger K, Chen J, Diamond JM, Li H, Collman RG, Bushman FD: Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts. PLoS One. 2012, 7: e42786-10.1371/journal.pone.0042786.
Article
PubMed Central
CAS
PubMed
Google Scholar
Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, Yadav A, Bushman FD, Collman RG: Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med. 2011, 184: 957-963. 10.1164/rccm.201104-0655OC.
Article
PubMed Central
PubMed
Google Scholar
Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L, Schmidt LA, Young VB, Toews GB, Curtis JL, Sundaram B, Martinez FJ, Huffnagle GB: Analysis of the lung microbiome in the “healthy” smoker and in COPD. PLoS One. 2011, 6: e16384-10.1371/journal.pone.0016384.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hilty M, Burke C, Pedro H, Cardenas P, Bush A, Bossley C, Davies J, Ervine A, Poulter L, Pachter L, Moffatt MF, Cookson WO: Disordered microbial communities in asthmatic airways. PLoS One. 2010, 5: e8578-10.1371/journal.pone.0008578.
Article
PubMed Central
PubMed
Google Scholar
Pragman AA, Kim HB, Reilly CS, Wendt C, Isaacson RE: The lung microbiome in moderate and severe chronic obstructive pulmonary disease. PLoS One. 2012, 7: e47305-10.1371/journal.pone.0047305.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lozupone C, Cota-Gomez A, Palmer BE, Linderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G, Campbell TB, Flores SC, Ackerman G, Stombaugh J, Ursell L, Beck JM, Curtis JL, Young VB, Lynch SV, Huang L, Weinstock GM, Knox KS, Twigg H, Morris A, Ghedin E, Bushman FD, Collman RG, Knight R, Fontenot AP, Lung HIV Microbiome Project: Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med. 2013, 187: 1110-1117. 10.1164/rccm.201211-2145OC.
Article
PubMed Central
PubMed
Google Scholar
Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM, Weinstock GM, Lung HIV Microbiome Project: Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med. 2013, 187: 1067-1075. 10.1164/rccm.201210-1913OC.
Article
PubMed Central
PubMed
Google Scholar
Monso E, Rosell A, Bonet G, Manterola J, Cardona PJ, Ruiz J, Morera J: Risk factors for lower airway bacterial colonization in chronic bronchitis. Eur Respir J. 1999, 13: 338-342. 10.1034/j.1399-3003.1999.13b20.x.
Article
CAS
PubMed
Google Scholar
Monso E, Ruiz J, Rosell A, Manterola J, Fiz J, Morera J, Ausina V: Bacterial infection in chronic obstructive pulmonary disease. A study of stable and exacerbated outpatients using the protected specimen brush. Am J Respir Crit Care Med. 1995, 152: 1316-1320. 10.1164/ajrccm.152.4.7551388.
Article
CAS
PubMed
Google Scholar
Zalacain R, Sobradillo V, Amilibia J, Barron J, Achotegui V, Pijoan JI, Llorente JL: Predisposing factors to bacterial colonization in chronic obstructive pulmonary disease. Eur Respir J. 1999, 13: 343-348. 10.1034/j.1399-3003.1999.13b21.x.
Article
CAS
PubMed
Google Scholar
Huang YJ, Lynch SV: The emerging relationship between the airway microbiota and chronic respiratory disease: clinical implications. Expert Rev Respir Med. 2011, 5: 809-821. 10.1586/ers.11.76.
Article
PubMed Central
PubMed
Google Scholar
Huang YJ, Nelson CE, Brodie EL, Desantis TZ, Baek MS, Liu J, Woyke T, Allgaier M, Bristow J, Wiener-Kronish JP, Sutherland ER, King TS, Icitovic N, Martin RJ, Calhoun WJ, Castro M, Denlinger LC, Dimango E, Kraft M, Peters SP, Wasserman SI, Wechsler ME, Boushey HA, Lynch SV, National Heart, Lung, and Blood Institute’s Asthma Clinical Research Network: Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma. J Allergy Clin Immunol. 2011, 127: 372-381. 10.1016/j.jaci.2010.10.048. e371-373
Article
PubMed Central
PubMed
Google Scholar
Gleeson K, Eggli DF, Maxwell SL: Quantitative aspiration during sleep in normal subjects. Chest. 1997, 111: 1266-1272. 10.1378/chest.111.5.1266.
Article
CAS
PubMed
Google Scholar
Cvejic L, Harding R, Churchward T, Turton A, Finlay P, Massey D, Bardin PG, Guy P: Laryngeal penetration and aspiration in individuals with stable COPD. Respirology. 2011, 16: 269-275. 10.1111/j.1440-1843.2010.01875.x.
Article
PubMed
Google Scholar
Rascon-Aguilar IE, Pamer M, Wludyka P, Cury J, Coultas D, Lambiase LR, Nahman NS, Vega KJ: Role of gastroesophageal reflux symptoms in exacerbations of COPD. Ches. 2006, 130: 1096-1101. 10.1378/chest.130.4.1096.
Article
Google Scholar
Sze MA, Dimitriu PA, Hayashi S, Elliott WM, McDonough JE, Gosselink JV, Cooper J, Sin DD, Mohn WW, Hogg JC: The lung tissue microbiome in chronic obstructive pulmonary disease. Am J Respir Crit Care Med. 2012, 185: 1073-1080. 10.1164/rccm.201111-2075OC.
Article
PubMed Central
PubMed
Google Scholar
Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SV: A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. OMICS. 2010, 14: 9-59. 10.1089/omi.2009.0100.
Article
PubMed Central
CAS
PubMed
Google Scholar
Baines KJ, Simpson JL, Gibson PG: Innate immune responses are increased in chronic obstructive pulmonary disease. PLoS One. 2011, 6: e18426-10.1371/journal.pone.0018426.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pace E, Ferraro M, Siena L, Melis M, Montalbano AM, Johnson M, Bonsignore MR, Bonsignore G, Gjomarkaj M: Cigarette smoke increases toll-like receptor 4 and modifies lipopolysaccharide-mediated responses in airway epithelial cells. Immunology. 2008, 124: 401-411. 10.1111/j.1365-2567.2007.02788.x.
Article
PubMed Central
CAS
PubMed
Google Scholar
Seemungal TA, Wilkinson TM, Hurst JR, Perera WR, Sapsford RJ, Wedzicha JA: Long-term erythromycin therapy is associated with decreased chronic obstructive pulmonary disease exacerbations. Am J Respir Crit Care Med. 2008, 178: 1139-1147. 10.1164/rccm.200801-145OC.
Article
CAS
PubMed
Google Scholar
Albert RK, Connett J, Bailey WC, Casaburi R, Cooper JA, Criner GJ, Curtis JL, Dransfield MT, Han MK, Lazarus SC, Make B, Marchetti N, Martinez FJ, Madinger NE, McEvoy C, Niewoehner DE, Porsasz J, Price CS, Reilly J, Scanlon PD, Sciurba FC, Scharf SM, Washko GR, Woodruff PG, Anthonisen NR, COPD Clinical Research Network: Azithromycin for prevention of exacerbations of COPD. N Engl J Med. 2011, 365: 689-698. 10.1056/NEJMoa1104623.
Article
PubMed Central
CAS
PubMed
Google Scholar
Documents ATS: ATS/ERS recommendations for standardized procedures for the online and offline measurement of exhaled lower respiratory nitric oxide and nasal nitric oxide, 2005. Am J Respir Crit Care Med. 2005, 171: 912-930.
Article
Google Scholar
Segal LN, Methe BA, Nolan A, Hoshino Y, Rom WN, Dawson R, Bateman E, Weiden MD: HIV-1 and bacterial pneumonia in the era of antiretroviral therapy. Proc Am Thorac Soc. 2011, 8: 282-287. 10.1513/pats.201006-044WR.
Article
PubMed Central
PubMed
Google Scholar
Fierer N, Hamady M, Lauber CL, Knight R: The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci USA. 2008, 105: 17994-17999. 10.1073/pnas.0807920105.
Article
PubMed Central
CAS
PubMed
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R: QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010, 7: 335-336. 10.1038/nmeth.f.303.
Article
PubMed Central
CAS
PubMed
Google Scholar
Edgar RC: Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010, 26: 2460-2461. 10.1093/bioinformatics/btq461.
Article
CAS
PubMed
Google Scholar
Wang Q, Garrity GM, Tiedje JM, Cole JR: Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007, 73: 5261-5267. 10.1128/AEM.00062-07.
Article
PubMed Central
CAS
PubMed
Google Scholar
Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R: PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics. 2010, 26: 266-267. 10.1093/bioinformatics/btp636.
Article
PubMed Central
CAS
PubMed
Google Scholar
Price MN, Dehal PS, Arkin AP: FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One. 2010, 5: e9490-10.1371/journal.pone.0009490.
Article
PubMed Central
PubMed
Google Scholar
Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R: UniFrac: an effective distance metric for microbial community comparison. ISME J. 2011, 5: 169-172. 10.1038/ismej.2010.133.
Article
PubMed Central
PubMed
Google Scholar
Reiner A, Yekutieli D, Benjamini Y: Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics. 2003, 19: 368-375. 10.1093/bioinformatics/btf877.
Article
CAS
PubMed
Google Scholar
Lozupone C, Knight R: UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005, 71: 8228-8235. 10.1128/AEM.71.12.8228-8235.2005.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dray SaD AB: The ade4 package: implementing the duality diagram for ecologists. J Stat Softw. 2007, 22: 1-20.
Google Scholar
Cailliez F: The analytical solution of the additive constant problem. Psychometrika. 1983, 48: 305-310. 10.1007/BF02294026.
Article
Google Scholar
DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL: NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 2006, 34: W394-399. 10.1093/nar/gkl244.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lemon KP, Klepac-Ceraj V, Schiffer HK, Brodie EL, Lynch SV, Kolter R: Comparative analyses of the bacterial microbiota of the human nostril and oropharynx. M Bio. 2010, 1: e00129-10.
PubMed Central
PubMed
Google Scholar
Charlson ES, Chen J, Custers-Allen R, Bittinger K, Li H, Sinha R, Hwang J, Bushman FD, Collman RG: Disordered microbial communities in the upper respiratory tract of cigarette smokers. PLoS One. 2010, 5: e15216-10.1371/journal.pone.0015216.
Article
PubMed Central
CAS
PubMed
Google Scholar
Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST: Bayesian community-wide culture-independent microbial source tracking. Nat Methods. 2011, 8: 761-763. 10.1038/nmeth.1650.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, Collman RG, Bushman FD, Li H: Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics. 2012, 28: 2106-2113. 10.1093/bioinformatics/bts342.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cosio MG, Saetta M, Agusti A: Immunologic aspects of chronic obstructive pulmonary disease. N Engl J Med. 2009, 360: 2445-2454. 10.1056/NEJMra0804752.
Article
CAS
PubMed
Google Scholar
Adrie C, Monchi M, Dinh-Xuan AT, Dall'Ava-Santucci J, Dhainaut JF, Pinsky MR: Exhaled and nasal nitric oxide as a marker of pneumonia in ventilated patients. Am J Respir Crit Care Med. 2001, 163: 1143-1149. 10.1164/ajrccm.163.5.9906049.
Article
CAS
PubMed
Google Scholar
Dressel H, de la Motte D, Reichert J, Ochmann U, Petru R, Angerer P, Holz O, Nowak D, Jorres RA: Exhaled nitric oxide: independent effects of atopy, smoking, respiratory tract infection, gender and height. Respir Med. 2008, 102: 962-969. 10.1016/j.rmed.2008.02.012.
Article
PubMed
Google Scholar
Soop A, Sollevi A, Weitzberg E, Lundberg JO, Palm J, Albert J: Exhaled NO and plasma cGMP increase after endotoxin infusion in healthy volunteers. Eur Respir J. 2003, 21: 594-599. 10.1183/09031936.03.00008603.
Article
CAS
PubMed
Google Scholar
Kharitonov SA, Robbins RA, Yates D, Keatings V, Barnes PJ: Acute and chronic effects of cigarette smoking on exhaled nitric oxide. Am J Respir Crit Care Med. 1995, 152: 609-612. 10.1164/ajrccm.152.2.7543345.
Article
CAS
PubMed
Google Scholar
Malinovschi A, Janson C, Holmkvist T, Norback D, Merilainen P, Hogman M: Effect of smoking on exhaled nitric oxide and flow-independent nitric oxide exchange parameters. Eur Respir J. 2006, 28: 339-345. 10.1183/09031936.06.00113705.
Article
CAS
PubMed
Google Scholar
Clunes LA, Davies CM, Coakley RD, Aleksandrov AA, Henderson AG, Zeman KL, Worthington EN, Gentzsch M, Kreda SM, Cholon D, Bennett WD, Riordan JR, Boucher RC, Tarran R: Cigarette smoke exposure induces CFTR internalization and insolubility, leading to airway surface liquid dehydration. FASEB J. 2012, 26: 533-545. 10.1096/fj.11-192377.
Article
PubMed Central
CAS
PubMed
Google Scholar
Simet SM, Sisson JH, Pavlik JA, Devasure JM, Boyer C, Liu X, Kawasaki S, Sharp JG, Rennard SI, Wyatt TA: Long-term cigarette smoke exposure in a mouse model of ciliated epithelial cell function. Am J Respir Cell Mol Biol. 2010, 43: 635-640. 10.1165/rcmb.2009-0297OC.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hodge S, Hodge G, Scicchitano R, Reynolds PN, Holmes M: Alveolar macrophages from subjects with chronic obstructive pulmonary disease are deficient in their ability to phagocytose apoptotic airway epithelial cells. Immunol Cell Biol. 2003, 81: 289-296. 10.1046/j.1440-1711.2003.t01-1-01170.x.
Article
PubMed
Google Scholar
Taylor AE, Finney-Hayward TK, Quint JK, Thomas CM, Tudhope SJ, Wedzicha JA, Barnes PJ, Donnelly LE: Defective macrophage phagocytosis of bacteria in COPD. Eur Respir J. 2010, 35: 1039-1047. 10.1183/09031936.00036709.
Article
CAS
PubMed
Google Scholar