{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T08:09:07Z","timestamp":1790323747523,"version":"4.1.0"},"reference-count":28,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2017,2,7]],"date-time":"2017-02-07T00:00:00Z","timestamp":1486425600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0170622","type":"journal-article","created":{"date-parts":[[2017,2,7]],"date-time":"2017-02-07T13:33:46Z","timestamp":1486474426000},"page":"e0170622","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":121,"title":["Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients"],"prefix":"10.1371","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4002-1506","authenticated-orcid":true,"given":"Michael J.","family":"Cox","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena M.","family":"Turek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Hennessy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ghazala K.","family":"Mirza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phillip L.","family":"James","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meg","family":"Coleman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Jones","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Wilson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diana","family":"Bilton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William O. C.","family":"Cookson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miriam F.","family":"Moffatt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael R.","family":"Loebinger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2017,2,7]]},"reference":[{"issue":"4","key":"ref1","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1378\/chest.10-0099","article-title":"Trends and Burden of Bronchiectasis-Associated Hospitalizations in the United States, 1993\u20132006","volume":"138","author":"AE Seitz","year":"2010","journal-title":"Chest"},{"issue":"Suppl 1","key":"ref2","doi-asserted-by":"crossref","first-page":"i1","DOI":"10.1136\/thx.2010.136119","article-title":"British Thoracic Society guideline for non-CFbronchiectasis","volume":"65","author":"MC Pasteur","year":"2010","journal-title":"Thorax"},{"issue":"1","key":"ref3","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1089\/omi.2009.0100","article-title":"A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations","volume":"14","author":"YJ Huang","year":"2010","journal-title":"OMICS"},{"issue":"2","key":"ref4","doi-asserted-by":"crossref","first-page":"e16384","DOI":"10.1371\/journal.pone.0016384","article-title":"Analysis of the Lung Microbiome in the \u201cHealthy\u201d Smoker and in COPD","volume":"6","author":"JR Erb-Downward","year":"2011","journal-title":"PLoS ONE"},{"issue":"7","key":"ref5","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1136\/thx.2010.137281","article-title":"Use of culture and molecular analysis to determine the effect of antibiotic treatment on microbial community diversity and abundance during exacerbation in patients with cystic fibrosis","volume":"66","author":"MM Tunney","year":"2011","journal-title":"Thorax"},{"issue":"6","key":"ref6","doi-asserted-by":"crossref","first-page":"e11044","DOI":"10.1371\/journal.pone.0011044","article-title":"Airway Microbiota and Pathogen Abundance in Age-Stratified Cystic Fibrosis Patients","volume":"5","author":"MJ Cox","year":"2010","journal-title":"PLoS ONE"},{"issue":"12","key":"ref7","doi-asserted-by":"crossref","first-page":"e15216","DOI":"10.1371\/journal.pone.0015216","article-title":"Disordered Microbial Communities in the Upper Respiratory Tract of Cigarette Smokers","volume":"5","author":"ES Charlson","year":"2010","journal-title":"PLoS ONE"},{"issue":"1","key":"ref8","doi-asserted-by":"crossref","first-page":"e8578","DOI":"10.1371\/journal.pone.0008578","article-title":"Disordered microbial communities in asthmatic airways","volume":"5","author":"M Hilty","year":"2010","journal-title":"PLoS ONE"},{"issue":"1","key":"ref9","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1471-2466-9-14","article-title":"Studying bacteria in respiratory specimens by using conventional and molecular microbiological approaches","volume":"9","author":"GB Rogers","year":"2009","journal-title":"BMC Pulm Med"},{"key":"ref10","article-title":"Longitudinal Analysis of the Non-Cystic Fibrosis Bronchiectasis Microbiome (ATS Journals)","author":"MJ Cox","year":"2015"},{"key":"ref11","article-title":"Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-CF bronchiectasis patients","author":"MJ Cox","year":"2016","journal-title":"bioRxiv"},{"key":"ref12","article-title":"Decade-long bacterial community dynamics in cystic fibrosis airways","author":"J Zhao","year":"2012","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"3","key":"ref13","doi-asserted-by":"crossref","first-page":"e32543","DOI":"10.1371\/journal.pone.0032543","article-title":"Improved Detection of Bifidobacteria with Optimised 16S rRNA-Gene Based Pyrosequencing","volume":"7","author":"K Sim","year":"2012","journal-title":"PLoS ONE"},{"issue":"46","key":"ref14","doi-asserted-by":"crossref","first-page":"17994","DOI":"10.1073\/pnas.0807920105","article-title":"The influence of sex, handedness, and washing on the diversity of hand surface bacteria","volume":"105","author":"N Fierer","year":"2008","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"4","key":"ref15","doi-asserted-by":"crossref","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data","volume":"8","author":"PJ McMurdie","year":"2013","journal-title":"PLoS ONE"},{"key":"ref16","unstructured":"Team RC. R: A language and environment for statistical computing [Internet]. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/R-project.org\" xlink:type=\"simple\">R-project.org<\/ext-link>. Vienna; 2014 [cited 2015 Jun 10]. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.R-project.org\/\" xlink:type=\"simple\">http:\/\/www.R-project.org\/<\/ext-link>"},{"issue":"10","key":"ref17","doi-asserted-by":"crossref","first-page":"4356","DOI":"10.1128\/AEM.66.10.4356-4360.2000","article-title":"PCR primers that amplify fungal rRNA genes from environmental samples","volume":"66","author":"J Borneman","year":"2000","journal-title":"Applied and Environmental Microbiology"},{"key":"ref18","article-title":"Outgrowth of the Bacterial Airway Microbiome following Rhinovirus Exacerbation of Chronic Obstructive Pulmonary Disease","author":"PL Molyneaux","year":"2013","journal-title":"American Journal of Respiratory and Critical Care Medicine"},{"issue":"8","key":"ref19","doi-asserted-by":"crossref","first-page":"e1005846","DOI":"10.1371\/journal.ppat.1005846","article-title":"Evidence and Role for Bacterial Mucin Degradation in Cystic Fibrosis Airway Disease","volume":"12","author":"JM Flynn","year":"2016","journal-title":"PLoS Pathog"},{"issue":"7","key":"ref20","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1056\/NEJMoa012561","article-title":"New strains of bacteria and exacerbations of chronic obstructive pulmonary disease","volume":"347","author":"S Sethi","year":"2002","journal-title":"N Engl J Med"},{"issue":"5","key":"ref21","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1002\/ppul.20794","article-title":"Predictors of mucoid Pseudomonas colonization in cystic fibrosis patients","volume":"43","author":"H Levy","year":"2008","journal-title":"Pediatr Pulmonol"},{"issue":"5","key":"ref22","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/j.jcf.2011.05.002","article-title":"Does bacterial density in cystic fibrosis sputum increase prior to pulmonary exacerbation?","volume":"10","author":"FA Stressmann","year":"2011","journal-title":"J Cyst Fibros"},{"issue":"10","key":"ref23","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.1164\/rccm.201210-1937OC","article-title":"Lung microbiota and bacterial abundance in patients with bronchiectasis when clinically stable and during exacerbation","volume":"187","author":"MM Tunney","year":"2013","journal-title":"American Journal of Respiratory and Critical Care Medicine"},{"issue":"3","key":"ref24","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1513\/AnnalsATS.201211-107OC","article-title":"Changes in Cystic Fibrosis Airway Microbiota at Pulmonary Exacerbation","volume":"10","author":"LA Carmody","year":"2013","journal-title":"Annals ATS"},{"issue":"1","key":"ref25","doi-asserted-by":"crossref","first-page":"5176","DOI":"10.1186\/s40168-015-0074-9","article-title":"The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation","volume":"3","author":"LA Carmody","year":"2015","journal-title":"Microbiome"},{"issue":"12","key":"ref26","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1016\/S2213-2600(14)70213-9","article-title":"The effect of long-term macrolide treatment on respiratory microbiota composition in non-cystic fibrosis bronchiectasis: an analysis from the randomised, double-blind, placebo-controlled BLESS trial","volume":"2","author":"GB Rogers","year":"2014","journal-title":"Lancet Respir Med"},{"issue":"8","key":"ref27","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1164\/rccm.201312-2208OC","article-title":"Inhaled colistin in patients with bronchiectasis and chronic Pseudomonas aeruginosa infection","volume":"189","author":"CS Haworth","year":"2014","journal-title":"American Journal of Respiratory and Critical Care Medicine"},{"key":"ref28","first-page":"1","article-title":"Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs","author":"P Jorth","year":"2015","journal-title":"Cell Host and Microbe"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0170622","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T23:51:30Z","timestamp":1540338690000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0170622"}},"subtitle":[],"editor":[{"given":"Marie-Joelle","family":"Virolle","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,2,7]]},"references-count":28,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2017,2,7]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0170622","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/050237","asserted-by":"object"}]},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,2,7]]}}}