{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T05:14:12Z","timestamp":1792300452345,"version":"4.4.0"},"reference-count":59,"publisher":"Springer Science and Business Media LLC","issue":"1","funder":[{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council (AU)","doi-asserted-by":"publisher","award":["1040830"],"award-info":[{"award-number":["1040830"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001075","name":"Channel 7 Children's Research Foundation (AU)","doi-asserted-by":"publisher","award":["12500"],"award-info":[{"award-number":["12500"]}],"id":[{"id":"10.13039\/501100001075","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Microbiome"],"published-print":{"date-parts":[[2016,12]]},"DOI":"10.1186\/s40168-016-0182-1","type":"journal-article","created":{"date-parts":[[2016,7,7]],"date-time":"2016-07-07T08:32:43Z","timestamp":1467880363000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":163,"title":["The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx"],"prefix":"10.1186","volume":"4","author":[{"given":"R. L.","family":"Marsh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M.","family":"Kaestli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A. B.","family":"Chang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. J.","family":"Binks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C. E.","family":"Pope","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L. R.","family":"Hoffman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H. C.","family":"Smith-Vaughan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,7,7]]},"reference":[{"issue":"2","key":"182_CR1","doi-asserted-by":"crossref","first-page":"e00037","DOI":"10.1128\/mBio.00037-15","volume":"6","author":"CM Bassis","year":"2015","unstructured":"Bassis CM, Erb-Downward JR, Dickson RP, Freeman CM, Schmidt TM, Young VB, et al. Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. MBio. 2015;6(2):e00037.","journal-title":"MBio"},{"issue":"9944","key":"182_CR2","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1016\/S0140-6736(14)61136-3","volume":"384","author":"RP Dickson","year":"2014","unstructured":"Dickson RP, Martinez FJ, Huffnagle GB. The role of the microbiome in exacerbations of chronic lung diseases. Lancet. 2014;384(9944):691\u2013702.","journal-title":"Lancet"},{"issue":"Suppl 1","key":"182_CR3","first-page":"6","volume":"16","author":"J Forton","year":"2015","unstructured":"Forton J. Induced sputum in young healthy children with cystic fibrosis. Paediatr Respir Rev. 2015;16 Suppl 1:6\u20138.","journal-title":"Paediatr Respir Rev"},{"issue":"11","key":"182_CR4","doi-asserted-by":"crossref","first-page":"1309","DOI":"10.1164\/rccm.201312-2129PP","volume":"189","author":"KL Whiteson","year":"2014","unstructured":"Whiteson KL, Bailey B, Bergkessel M, Conrad D, Delhaes L, Felts B, et al. The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis. Parallels from island biogeography. Am J Respir Crit Care Med. 2014;189(11):1309\u201315.","journal-title":"Am J Respir Crit Care Med"},{"issue":"7","key":"182_CR5","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1513\/AnnalsATS.201312-456OC","volume":"11","author":"CJ Gast van der","year":"2014","unstructured":"van der Gast CJ, Cuthbertson L, Rogers GB, Pope C, Marsh RL, Redding GJ, et al. Three clinically distinct chronic pediatric airway infections share a common core microbiota. Ann Am Thorac Soc. 2014;11(7):1039\u201348.","journal-title":"Ann Am Thorac Soc"},{"issue":"5","key":"182_CR6","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1002\/(SICI)1099-0496(199605)21:5<267::AID-PPUL1>3.0.CO;2-K","volume":"21","author":"DS Armstrong","year":"1996","unstructured":"Armstrong DS, Grimwood K, Carlin JB, Carzino R, Olinsky A, Phelan PD. Bronchoalveolar lavage or oropharyngeal cultures to identify lower respiratory pathogens in infants with cystic fibrosis. Pediatr Pulmonol. 1996;21(5):267\u201375.","journal-title":"Pediatr Pulmonol"},{"key":"182_CR7","doi-asserted-by":"crossref","first-page":"48","DOI":"10.15172\/pneu.2015.6\/636","volume":"6","author":"AB Chang","year":"2015","unstructured":"Chang AB, Smith-Vaughan HC, Sloots TP, Valery PC, Whiley D, Beissbarth J, et al. Upper airway viruses and bacteria detection in clinical pneumonia in a population with high nasal colonisation do not relate to clinical signs. Pneumonia. 2015;6:48\u201356.","journal-title":"Pneumonia"},{"issue":"2","key":"182_CR8","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1513\/AnnalsATS.201407-310OC","volume":"12","author":"ET Zemanick","year":"2015","unstructured":"Zemanick ET, Wagner BD, Robertson CE, Stevens MJ, Szefler SJ, Accurso FJ, et al. Assessment of airway microbiota and inflammation in cystic fibrosis using multiple sampling methods. Ann Am Thorac Soc. 2015;12(2):221\u20139.","journal-title":"Ann Am Thorac Soc"},{"issue":"7","key":"182_CR9","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1513\/AnnalsATS.201311-383OC","volume":"11","author":"PS Brown","year":"2014","unstructured":"Brown PS, Pope CE, Marsh RL, Qin X, McNamara S, Gibson R, et al. Directly sampling the lung of a young child with cystic fibrosis reveals diverse microbiota. Ann Am Thorac Soc. 2014;11(7):1049\u201355.","journal-title":"Ann Am Thorac Soc"},{"issue":"7","key":"182_CR10","doi-asserted-by":"crossref","first-page":"2601","DOI":"10.1128\/JCM.02282-05","volume":"44","author":"GB Rogers","year":"2006","unstructured":"Rogers GB, Carroll MP, Serisier DJ, Hockey PM, Jones G, Kehagia V, et al. Use of 16S rRNA gene profiling by terminal restriction fragment length polymorphism analysis to compare bacterial communities in sputum and mouthwash samples from patients with cystic fibrosis. J Clin Microbiol. 2006;44(7):2601\u20134.","journal-title":"J Clin Microbiol"},{"issue":"34","key":"182_CR11","doi-asserted-by":"crossref","first-page":"13769","DOI":"10.1073\/pnas.1107435109","volume":"109","author":"AF Goddard","year":"2012","unstructured":"Goddard AF, Staudinger BJ, Dowd SE, Joshi-Datar A, Wolcott RD, Aitken ML, et al. Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota. PNAS. 2012;109(34):13769\u201374.","journal-title":"PNAS"},{"key":"182_CR12","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/2049-2618-2-29","volume":"2","author":"LE Botero","year":"2014","unstructured":"Botero LE, Delgado-Serrano L, Cepeda ML, Bustos JR, Anzola JM, Del Portillo P, et al. Respiratory tract clinical sample selection for microbiota analysis in patients with pulmonary tuberculosis. Microbiome. 2014;2:29.","journal-title":"Microbiome"},{"issue":"1","key":"182_CR13","doi-asserted-by":"crossref","first-page":"e0116029","DOI":"10.1371\/journal.pone.0116029","volume":"10","author":"S Boutin","year":"2015","unstructured":"Boutin S, Graeber SY, Weitnauer M, Panitz J, Stahl M, Clausznitzer D, et al. Comparison of microbiomes from different niches of upper and lower airways in children and adolescents with cystic fibrosis. PLoS One. 2015;10(1):e0116029.","journal-title":"PLoS One"},{"issue":"11","key":"182_CR14","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1164\/rccm.201407-1240OC","volume":"190","author":"G Biesbroek","year":"2014","unstructured":"Biesbroek G, Tsivtsivadze E, Sanders EA, Montijn R, Veenhoven RH, Keijser BJ, et al. Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children. Am J Respir Crit Care Med. 2014;190(11):1283\u201392.","journal-title":"Am J Respir Crit Care Med"},{"issue":"1","key":"182_CR15","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1186\/1471-2334-10-304","volume":"10","author":"G Mackenzie","year":"2010","unstructured":"Mackenzie G, Leach A, Carapetis J, Fisher J, Morris P. Epidemiology of nasopharyngeal carriage of respiratory bacterial pathogens in children and adults: cross-sectional surveys in a population with high rates of pneumococcal disease. BMC Infect Dis. 2010;10(1):304.","journal-title":"BMC Infect Dis"},{"issue":"6","key":"182_CR16","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1016\/j.jpeds.2010.06.002","volume":"157","author":"KM Hare","year":"2010","unstructured":"Hare KM, Grimwood K, Leach AJ, Smith-Vaughan H, Torzillo PJ, Morris PS, et al. Respiratory bacterial pathogens in the nasopharynx and lower airways of Australian indigenous children with bronchiectasis. J Pediatr. 2010;157(6):1001\u20135.","journal-title":"J Pediatr"},{"issue":"5","key":"182_CR17","doi-asserted-by":"crossref","first-page":"1590","DOI":"10.1128\/JCM.03280-13","volume":"52","author":"O Sakwinska","year":"2014","unstructured":"Sakwinska O, Bastic Schmid V, Berger B, Bruttin A, Keitel K, Lepage M, et al. Nasopharyngeal microbiota in healthy children and pneumonia patients. J Clin Microbiol. 2014;52(5):1590\u20134.","journal-title":"J Clin Microbiol"},{"issue":"5","key":"182_CR18","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1016\/j.chom.2015.03.008","volume":"17","author":"SM Teo","year":"2015","unstructured":"Teo SM, Mok D, Pham K, Kusel M, Serralha M, Troy N, et al. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host Microbe. 2015;17(5):704\u201315.","journal-title":"Cell Host Microbe"},{"issue":"10","key":"182_CR19","doi-asserted-by":"crossref","first-page":"e46803","DOI":"10.1371\/journal.pone.0046803","volume":"7","author":"PA Cardenas","year":"2012","unstructured":"Cardenas PA, Cooper PJ, Cox MJ, Chico M, Arias C, Moffatt MF, et al. Upper airways microbiota in antibiotic-naive wheezing and healthy infants from the tropics of rural Ecuador. PLoS One. 2012;7(10):e46803.","journal-title":"PLoS One"},{"issue":"10","key":"182_CR20","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1164\/rccm.201302-0215OC","volume":"188","author":"NH Vissing","year":"2013","unstructured":"Vissing NH, Chawes BL, Bisgaard H. Increased risk of pneumonia and bronchiolitis after bacterial colonization of the airways as neonates. Am J Respir Crit Care Med. 2013;188(10):1246\u201352.","journal-title":"Am J Respir Crit Care Med"},{"key":"182_CR21","doi-asserted-by":"crossref","first-page":"c4978","DOI":"10.1136\/bmj.c4978","volume":"341","author":"H Bisgaard","year":"2010","unstructured":"Bisgaard H, Hermansen MN, Bonnelykke K, Stokholm J, Baty F, Skytt NL, et al. Association of bacteria and viruses with wheezy episodes in young children: prospective birth cohort study. BMJ. 2010;341:c4978.","journal-title":"BMJ"},{"key":"182_CR22","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1472-6815-12-11","volume":"12","author":"RL Marsh","year":"2012","unstructured":"Marsh RL, Binks MJ, Beissbarth J, Christensen P, Morris PS, Leach AJ, et al. Quantitative PCR of ear discharge from indigenous Australian children with acute otitis media with perforation supports a role for Alloiococcus otitidis as a secondary pathogen. BMC Ear Nose Throat Disord. 2012;12:11.","journal-title":"BMC Ear Nose Throat Disord"},{"issue":"1","key":"182_CR23","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1099\/00221287-148-1-257","volume":"148","author":"MA Nadkarni","year":"2002","unstructured":"Nadkarni MA, Martin FE, Jacques NA, Hunter N. Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology. 2002;148(1):257\u201366.","journal-title":"Microbiology"},{"key":"182_CR24","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/s12915-014-0087-z","volume":"12","author":"SJ Salter","year":"2014","unstructured":"Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12:87.","journal-title":"BMC Biol"},{"issue":"3","key":"182_CR25","doi-asserted-by":"crossref","first-page":"e32942","DOI":"10.1371\/journal.pone.0032942","volume":"7","author":"G Biesbroek","year":"2012","unstructured":"Biesbroek G, Sanders EAM, Roeselers G, Wang X, Caspers MPM, Trzci\u0144ski K, et al. Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection. PLoS One. 2012;7(3):e32942.","journal-title":"PLoS One"},{"key":"182_CR26","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/s40168-015-0083-8","volume":"3","author":"J Jervis-Bardy","year":"2015","unstructured":"Jervis-Bardy J, Leong LE, Marri S, Smith RJ, Choo JM, Smith-Vaughan HC, et al. Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data. Microbiome. 2015;3:19.","journal-title":"Microbiome"},{"key":"182_CR27","volume-title":"PERMANOVA+ for PRIMER: guide to software and statistical methods","author":"M Anderson","year":"2008","unstructured":"Anderson M, Gorley R, Clarke K. PERMANOVA+ for PRIMER: guide to software and statistical methods. 2008."},{"issue":"7","key":"182_CR28","doi-asserted-by":"crossref","first-page":"e1004923","DOI":"10.1371\/journal.ppat.1004923","volume":"11","author":"RP Dickson","year":"2015","unstructured":"Dickson RP, Huffnagle GB. The lung microbiome: new principles for respiratory bacteriology in health and disease. PLoS Pathog. 2015;11(7):e1004923.","journal-title":"PLoS Pathog"},{"issue":"2","key":"182_CR29","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1111\/j.1365-2222.2006.02423.x","volume":"36","author":"WA Balemans","year":"2006","unstructured":"Balemans WA, Rovers MM, Schilder AG, Sanders EA, Kimpen JL, Zielhuis GA, et al. Recurrent childhood upper respiratory tract infections do not reduce the risk of adult atopic disease. Clin Exp Allergy. 2006;36(2):198\u2013203.","journal-title":"Clin Exp Allergy"},{"issue":"4","key":"182_CR30","first-page":"510","volume":"28","author":"S Lambert","year":"2004","unstructured":"Lambert S, O\u2019Grady KA, Gabriel S, Carter R, Nolan T. The cost of seasonal respiratory illnesses in Australian children: the dominance of patient and family costs and implications for vaccine use. Commun Dis Intell Q Rep. 2004;28(4):510\u20136.","journal-title":"Commun Dis Intell Q Rep"},{"issue":"9","key":"182_CR31","doi-asserted-by":"crossref","first-page":"e75558","DOI":"10.1371\/journal.pone.0075558","volume":"8","author":"A Odutola","year":"2013","unstructured":"Odutola A, Antonio M, Owolabi O, Bojang A, Foster-Nyarko E, Donkor S, et al. Comparison of the prevalence of common bacterial pathogens in the oropharynx and nasopharynx of Gambian infants. PLoS One. 2013;8(9):e75558.","journal-title":"PLoS One"},{"key":"182_CR32","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1186\/1471-2334-13-357","volume":"13","author":"H Chappuy","year":"2013","unstructured":"Chappuy H, Keitel K, Gehri M, Tabin R, Robitaille L, Raymond F, et al. Nasopharyngeal carriage of individual Streptococcus pneumoniae serotypes during pediatric radiologically confirmed community acquired pneumonia following PCV7 introduction in Switzerland. BMC Infect Dis. 2013;13:357.","journal-title":"BMC Infect Dis"},{"issue":"4","key":"182_CR33","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1016\/j.jaci.2013.10.049","volume":"133","author":"ER Hyde","year":"2014","unstructured":"Hyde ER, Petrosino JF, Piedra PA, Camargo Jr CA, Espinola JA, Mansbach JM. Nasopharyngeal Proteobacteria are associated with viral etiology and acute wheezing in children with severe bronchiolitis. J Allergy Clin Immunol. 2014;133(4):1220\u20132.","journal-title":"J Allergy Clin Immunol"},{"issue":"6","key":"182_CR34","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1016\/j.jcf.2013.02.004","volume":"12","author":"O Ciofu","year":"2013","unstructured":"Ciofu O, Johansen HK, Aanaes K, Wassermann T, Alhede M, von Buchwald C, et al. P. aeruginosa in the paranasal sinuses and transplanted lungs have similar adaptive mutations as isolates from chronically infected CF lungs. J Cyst Fibros. 2013;12(6):729\u201336.","journal-title":"J Cyst Fibros"},{"issue":"Suppl 2","key":"182_CR35","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1016\/S1569-1993(13)00150-1","volume":"12","author":"K Aanaes","year":"2013","unstructured":"Aanaes K. Bacterial sinusitis can be a focus for initial lung colonisation and chronic lung infection in patients with cystic fibrosis. J Cyst Fibros. 2013;12 Suppl 2:S1\u201320.","journal-title":"J Cyst Fibros"},{"issue":"11","key":"182_CR36","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1097\/00006454-199411000-00009","volume":"13","author":"AJ Leach","year":"1994","unstructured":"Leach AJ, Boswell JB, Asche V, Nienhuys TG, Mathews JD. Bacterial colonization of the nasopharynx predicts very early onset and persistence of otitis media in Australian aboriginal infants. Pediatr Infect Dis J. 1994;13(11):983\u20139.","journal-title":"Pediatr Infect Dis J"},{"issue":"6","key":"182_CR37","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/1472-6815-6-10","volume":"10","author":"H Smith-Vaughan","year":"2006","unstructured":"Smith-Vaughan H, Byun R, Nadkarni M, Jacques NA, Hunter N, Halpin S, et al. Measuring nasal bacterial load and its association with otitis media. BMC Ear Nose Throat Disord. 2006;10(6):10.","journal-title":"BMC Ear Nose Throat Disord"},{"issue":"4","key":"182_CR38","first-page":"325","volume":"15","author":"AB Chang","year":"2014","unstructured":"Chang AB, Brown N, Toombs M, Marsh RL, Redding GJ. Lung disease in indigenous children. Paediatr Respir Rev. 2014;15(4):325\u201332.","journal-title":"Paediatr Respir Rev"},{"issue":"6","key":"182_CR39","doi-asserted-by":"crossref","first-page":"e0128064","DOI":"10.1371\/journal.pone.0128064","volume":"10","author":"LM Feazel","year":"2015","unstructured":"Feazel LM, Santorico SA, Robertson CE, Bashraheil M, Scott JA, Frank DN, et al. Effects of vaccination with 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV) on the nasopharyngeal microbiome of Kenyan toddlers. PLoS One. 2015;10(6):e0128064.","journal-title":"PLoS One"},{"issue":"4","key":"182_CR40","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1016\/j.jaci.2014.12.1909","volume":"135","author":"M Mika","year":"2015","unstructured":"Mika M, Mack I, Korten I, Qi W, Aebi S, Frey U, et al. Dynamics of the nasal microbiota in infancy: a prospective cohort study. J Allergy Clin Immunol. 2015;135(4):905\u201312. e11.","journal-title":"J Allergy Clin Immunol"},{"issue":"4","key":"182_CR41","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1016\/S0002-9343(00)00507-6","volume":"109","author":"AT Hill","year":"2000","unstructured":"Hill AT, Campbell EJ, Hill SL, Bayley DL, Stockley RA. Association between airway bacterial load and markers of airway inflammation in patients with stable chronic bronchitis. Am J Med. 2000;109(4):288\u201395.","journal-title":"Am J Med"},{"issue":"5","key":"182_CR42","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1164\/rccm.201509-1759OC","volume":"193","author":"SM Prevaes","year":"2016","unstructured":"Prevaes SM, de Winter-de Groot KM, Janssens HM, de Steenhuijsen Piters WA, Tramper-Stranders GA, Wyllie AL, et al. Development of the nasopharyngeal microbiota in infants with cystic fibrosis. Am J Respir Crit Care Med. 2016;193(5):504\u201315.","journal-title":"Am J Respir Crit Care Med"},{"issue":"3","key":"182_CR43","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1128\/JCM.39.3.1021-1024.2001","volume":"39","author":"KL O\u2019Brien","year":"2001","unstructured":"O\u2019Brien KL, Bronsdon MA, Dagan R, Yagupsky P, Janco J, Elliott J, et al. Evaluation of a medium (STGG) for transport and optimal recovery of Streptococcus pneumoniae from nasopharyngeal secretions collected during field studies. J Clin Microbiol. 2001;39(3):1021\u20134.","journal-title":"J Clin Microbiol"},{"issue":"1","key":"182_CR44","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.vaccine.2013.08.062","volume":"32","author":"C Satzke","year":"2013","unstructured":"Satzke C, Turner P, Virolainen-Julkunen A, Adrian PV, Antonio M, Hare KM, et al. Standard method for detecting upper respiratory carriage of Streptococcus pneumoniae: updated recommendations from the World Health Organization Pneumococcal Carriage Working Group. Vaccine. 2013;32(1):165\u201379.","journal-title":"Vaccine"},{"issue":"6","key":"182_CR45","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1378\/chest.13-2442","volume":"145","author":"DF Wurzel","year":"2014","unstructured":"Wurzel DF, Marchant JM, Yerkovich ST, Upham JW, Mackay IM, Masters IB, et al. Prospective characterization of protracted bacterial bronchitis in children. Chest. 2014;145(6):1271\u20138.","journal-title":"Chest"},{"issue":"6","key":"182_CR46","doi-asserted-by":"crossref","first-page":"356","DOI":"10.5694\/j.1326-5377.2010.tb03949.x","volume":"193","author":"AB Chang","year":"2010","unstructured":"Chang AB, Bell SC, Byrnes CA, Grimwood K, Holmes PW, King PT, et al. Chronic suppurative lung disease and bronchiectasis in children and adults in Australia and New Zealand. Med J Aust. 2010;193(6):356\u201365.","journal-title":"Med J Aust"},{"issue":"6","key":"182_CR47","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.1378\/chest.10-1763","volume":"139","author":"N Kapur","year":"2011","unstructured":"Kapur N, Masel JP, Watson D, Masters IB, Chang AB. Bronchoarterial ratio on high-resolution CT scan of the chest in children without pulmonary pathology: need to redefine bronchial dilatation. Chest. 2011;139(6):1445\u201350.","journal-title":"Chest"},{"issue":"1","key":"182_CR48","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1002\/ppul.22544","volume":"48","author":"SJ Pizzutto","year":"2012","unstructured":"Pizzutto SJ, Grimwood K, Bauert P, Schutz KL, Yerkovich ST, Upham JW, et al. Bronchoscopy contributes to the clinical management of indigenous children newly diagnosed with bronchiectasis. Pediatr Pulmonol. 2012;48(1):67\u201373.","journal-title":"Pediatr Pulmonol"},{"issue":"4","key":"182_CR49","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1016\/j.jpeds.2012.03.049","volume":"161","author":"AB Chang","year":"2012","unstructured":"Chang AB, Yerkovich ST, Gibson PG, Anderson-James S, Petsky HL, Carroll ML, et al. Pulmonary innate immunity in children with protracted bacterial bronchitis. J Pediatr. 2012;161(4):621\u20135.","journal-title":"J Pediatr"},{"issue":"1","key":"182_CR50","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1183\/09031936.00.15121700","volume":"15","author":"J Blic de","year":"2000","unstructured":"de Blic J, Midulla F, Barbato A, Clement A, Dab I, Eber E, et al. Bronchoalveolar lavage in children. ERS Task Force on bronchoalveolar lavage in children. European Respiratory Society. Eur Res J. 2000;15(1):217\u201331.","journal-title":"Eur Res J"},{"issue":"23","key":"182_CR51","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","volume":"75","author":"PD Schloss","year":"2009","unstructured":"Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537\u201341.","journal-title":"Appl Environ Microbiol"},{"issue":"12","key":"182_CR52","doi-asserted-by":"crossref","first-page":"e27310","DOI":"10.1371\/journal.pone.0027310","volume":"6","author":"PD Schloss","year":"2011","unstructured":"Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One. 2011;6(12):e27310.","journal-title":"PLoS One"},{"key":"182_CR53","unstructured":"Mothur 454-SOP. http:\/\/www.mothur.org\/wiki\/454_SOP . Accessed May 2014."},{"key":"182_CR54","unstructured":"Mothur Silve Reference Files. http:\/\/mothur.org\/wiki\/Silva_reference_files . Accessed May 2014."},{"key":"182_CR55","unstructured":"BLASTn. http:\/\/blast.ncbi.nlm.nih.gov\/Blast.cgi . Accessed Sept 2015."},{"key":"182_CR56","unstructured":"R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https:\/\/www.R-project.org\/ ."},{"key":"182_CR57","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-98141-3","volume-title":"ggplot2: elegant graphics for data analysis","author":"H Wickham","year":"2009","unstructured":"Wickham H. ggplot2: elegant graphics for data analysis. New York: Springer-Verlag; 2009."},{"key":"182_CR58","unstructured":"Eklund A. beeswarm: the bee swarm plot, an alternative to stripchart. R package version 0.2.1 https:\/\/CRAN.R-project.org\/package=beeswarm ."},{"key":"182_CR59","volume-title":"PRIMER v6: user manual\/tutorial","author":"K Clarke","year":"2006","unstructured":"Clarke K, Gorley R. PRIMER v6: user manual\/tutorial. Plymouth: PRIMER-E; 2006."}],"container-title":["Microbiome"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-016-0182-1","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,23]],"date-time":"2020-09-23T15:23:01Z","timestamp":1600874581000},"score":1,"resource":{"primary":{"URL":"http:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-016-0182-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,7,7]]},"references-count":59,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2016,12]]}},"alternative-id":["182"],"URL":"https:\/\/doi.org\/10.1186\/s40168-016-0182-1","relation":{},"ISSN":["2049-2618"],"issn-type":[{"value":"2049-2618","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,7,7]]},"article-number":"37"}}