{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T08:33:44Z","timestamp":1777624424382,"version":"3.51.4"},"reference-count":28,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2018,8,2]],"date-time":"2018-08-02T00:00:00Z","timestamp":1533168000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100012147","name":"Royal Brompton and Harefield NHS Foundation Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012147","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0201156","type":"journal-article","created":{"date-parts":[[2018,8,2]],"date-time":"2018-08-02T14:24:33Z","timestamp":1533219873000},"page":"e0201156","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":29,"title":["Comparison of the upper and lower airway microbiota in children with chronic lung diseases"],"prefix":"10.1371","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6353-3136","authenticated-orcid":true,"given":"Bushra","family":"Ahmed","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4002-1506","authenticated-orcid":true,"given":"Michael J.","family":"Cox","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leah","family":"Cuthbertson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Phillip L.","family":"James","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William O. C.","family":"Cookson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jane C.","family":"Davies","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Miriam F.","family":"Moffatt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew","family":"Bush","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2018,8,2]]},"reference":[{"key":"ref1","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"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1038\/ismej.2010.175","article-title":"Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities","volume":"5","author":"CJ van der Gast","year":"2011","journal-title":"ISME J"},{"key":"ref3","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"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/1465-9921-6-49","article-title":"Bacterial activity in cystic fibrosis lung infections","volume":"6","author":"GB Rogers","year":"2005","journal-title":"Respir Res"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"e0167649","DOI":"10.1371\/journal.pone.0167649","article-title":"Airway Microbiota in Bronchoalveolar Lavage Fluid from Clinically Well Infants with Cystic Fibrosis","volume":"11","author":"TA Laguna","year":"2016","journal-title":"PLoS One"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1104","DOI":"10.1136\/thoraxjnl-2016-209279","article-title":"The lower airway microbiota in early cystic fibrosis lung disease: a longitudinal analysis","volume":"72","author":"KB Frayman","year":"2017","journal-title":"Thorax"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1016\/S2213-2600(16)30081-9","article-title":"The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study","volume":"4","author":"M Mika","year":"2016","journal-title":"Lancet Respir Med"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1164\/rccm.201509-1759OC","article-title":"Development of the Nasopharyngeal Microbiota in Infants with Cystic Fibrosis","volume":"193","author":"SM Prevaes","year":"2016","journal-title":"Am J Respir Crit Care Med"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1164\/rccm.201407-1240OC","article-title":"Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children","volume":"190","author":"G Biesbroek","year":"2014","journal-title":"Am J Respir Crit Care Med"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"e0116029","DOI":"10.1371\/journal.pone.0116029","article-title":"Comparison of Microbiomes from Different Niches of Upper and Lower Airways in Children and Adolescents with Cystic Fibrosis","volume":"10","author":"S Boutin","year":"2015","journal-title":"PLoS ONE"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1002\/(SICI)1099-0496(199605)21:5<267::AID-PPUL1>3.0.CO;2-K","article-title":"Bronchoalveolar lavage or oropharyngeal cultures to identify lower respiratory pathogens in infants with cystic fibrosis","volume":"21","author":"DS Armstrong","year":"1996","journal-title":"Pediatr Pulmonol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1457","DOI":"10.1183\/09031936.02.00268002","article-title":"Sequential genotyping of Pseudomonas aeruginosa from upper and lower airways of cystic fibrosis patients","volume":"20","author":"A Jung","year":"2002","journal-title":"European Respiratory Journal"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1164\/rccm.201104-0655OC","article-title":"Topographical continuity of bacterial populations in the healthy human respiratory tract","volume":"184","author":"ES Charlson","year":"2011","journal-title":"Am J Respir Crit Care Med"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/nar\/gks808","article-title":"Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies","volume":"41","author":"A Klindworth","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"5112","DOI":"10.1128\/AEM.01043-13","article-title":"Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform","volume":"79","author":"JJ Kozich","year":"2013","journal-title":"Appl Environ Microbiol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1111\/j.1654-1103.2003.tb02228.x","article-title":"VEGAN, a package for R functions for commnity ecology","volume":"14","author":"P Dixon","year":"2003","journal-title":"Journal of Vegetation Science"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1576","DOI":"10.1128\/AEM.01996-06","article-title":"Quantitative and Qualitative \u03b2 Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities","volume":"73","author":"CA Lozupone","year":"2007","journal-title":"Applied and Environmental Microbiology"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1016\/j.jpeds.2008.05.005","article-title":"Guidelines for diagnosis of cystic fibrosis in newborns through older adults: Cystic Fibrosis Foundation consensus report","volume":"153","author":"PM Farrell","year":"2008","journal-title":"J Pediatr"},{"key":"ref19","doi-asserted-by":"crossref","DOI":"10.1183\/13993003.01090-2016","article-title":"European Respiratory Society guidelines for the diagnosis of primary ciliary dyskinesia","volume":"49","author":"JS Lucas","year":"2017","journal-title":"Eur Respir J"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1002\/ppul.21434","article-title":"Bronchoscopy in cystic fibrosis infants diagnosed by newborn screening","volume":"46","author":"P Stafler","year":"2011","journal-title":"Pediatr Pulmonol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/s12915-014-0087-z","article-title":"Reagent and laboratory contamination can critically impact sequence-based microbiome analyses","volume":"12","author":"SJ Salter","year":"2014","journal-title":"BMC Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature13786","article-title":"Biogeography and individuality shape function in the human skin metagenome","volume":"514","author":"J Oh","year":"2014","journal-title":"Nature"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1038\/nature07540","article-title":"A core gut microbiome in obese and lean twins","volume":"457","author":"PJ Turnbaugh","year":"2009","journal-title":"Nature"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"564","DOI":"10.3389\/fmicb.2016.00564","article-title":"Individuality, Stability, and Variability of the Plaque Microbiome","volume":"7","author":"DR Utter","year":"2016","journal-title":"Frontiers in Microbiology"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/s40168-016-0182-1","article-title":"The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx","volume":"4","author":"RL Marsh","year":"2016","journal-title":"Microbiome"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1038\/nmeth.1499","article-title":"Microbial community resemblance methods differ in their ability to detect biologically relevant patterns","volume":"7","author":"J Kuczynski","year":"2010","journal-title":"Nat Methods"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"e17035","DOI":"10.1371\/journal.pone.0017035","article-title":"Variability and Diversity of Nasopharyngeal Microbiota in Children","volume":"6","author":"D Bogaert","year":"2011","journal-title":"A Metagenomic Analysis. PLOS ONE"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1183\/09031936.01.17202810","article-title":"Interlobar differences in bronchoalveolar lavage fluid from children with cystic fibrosis","volume":"17","author":"JP Gutierrez","year":"2001","journal-title":"European Respiratory Journal"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0201156","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T11:05:04Z","timestamp":1540292704000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0201156"}},"subtitle":[],"editor":[{"given":"Alexander","family":"Larcombe","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,8,2]]},"references-count":28,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2018,8,2]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0201156","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,8,2]]}}}