{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T16:17:12Z","timestamp":1787674632261,"version":"build-2784847793"},"reference-count":51,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,3,25]],"date-time":"2024-03-25T00:00:00Z","timestamp":1711324800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,3,25]],"date-time":"2024-03-25T00:00:00Z","timestamp":1711324800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100000292","name":"Cystic Fibrosis Trust","doi-asserted-by":"publisher","award":["VIA 045"],"award-info":[{"award-number":["VIA 045"]}],"id":[{"id":"10.13039\/501100000292","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000292","name":"Cystic Fibrosis Trust","doi-asserted-by":"publisher","award":["VIA 045"],"award-info":[{"award-number":["VIA 045"]}],"id":[{"id":"10.13039\/501100000292","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000292","name":"Cystic Fibrosis Trust","doi-asserted-by":"publisher","award":["VIA 045"],"award-info":[{"award-number":["VIA 045"]}],"id":[{"id":"10.13039\/501100000292","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000292","name":"Cystic Fibrosis Trust","doi-asserted-by":"publisher","award":["VIA 045"],"award-info":[{"award-number":["VIA 045"]}],"id":[{"id":"10.13039\/501100000292","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000272","name":"National Institute for Health and Care Research","doi-asserted-by":"publisher","award":["CS012\u201313"],"award-info":[{"award-number":["CS012\u201313"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000272","name":"National Institute for Health and Care Research","doi-asserted-by":"publisher","award":["CS012\u201313"],"award-info":[{"award-number":["CS012\u201313"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000272","name":"National Institute for Health and Care Research","doi-asserted-by":"publisher","award":["CS012\u201313"],"award-info":[{"award-number":["CS012\u201313"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Microbiome"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Chronic infection and consequent airway inflammation are the leading causes of morbidity and early mortality for people living with cystic fibrosis (CF). However, lower airway infections across a range of chronic respiratory diseases, including in CF, do not follow classical \u2018one microbe, one disease\u2019 concepts of infection pathogenesis. Instead, they are comprised of diverse and temporally dynamic lung infection microbiota. Consequently, temporal dynamics need to be considered when attempting to associate lung microbiota with changes in disease status. Set within an island biogeography framework, we aimed to determine the ecological patterns and processes of temporal turnover within the lung microbiota of 30 paediatric and adult CF patients prospectively sampled over a 3-year period. Moreover, we aimed to ascertain the contributions of constituent chronic and intermittent colonizers on turnover within the wider microbiota.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The lung microbiota within individual patients was partitioned into constituent chronic and intermittent colonizing groups using the Leeds criteria and visualised with persistence-abundance relationships. This revealed bacteria chronically infecting a patient were both persistent and common through time, whereas intermittently infecting taxa were infrequent and rare; respectively representing the resident and transient portions of the wider microbiota. It also indicated that the extent of chronic colonization was far greater than could be appreciated with microbiological culture alone. Using species-time relationships to measure temporal turnover and Vellend\u2019s rationalized ecological processes demonstrated turnover in the resident chronic infecting groups was conserved and underpinned principally by the deterministic process of homogenizing dispersal. Conversely, intermittent colonizing groups, representing newly arrived immigrants and transient species, drove turnover in the wider microbiota and were predominately underpinned by the stochastic process of drift. For adult patients, homogenizing dispersal and drift were found to be significantly associated with lung function. Where a greater frequency of homogenizing dispersal was observed with worsening lung function and conversely drift increased with better lung function.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Our work provides a novel ecological framework for understanding the temporal dynamics of polymicrobial infection in CF that has translational potential to guide and improve therapeutic targeting of lung microbiota in CF and across a range of chronic airway diseases.<\/jats:p>\n                \n              <\/jats:sec>","DOI":"10.1186\/s40168-024-01780-6","type":"journal-article","created":{"date-parts":[[2024,3,25]],"date-time":"2024-03-25T05:10:53Z","timestamp":1711343453000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Ecological patterns and processes of temporal turnover within lung infection microbiota"],"prefix":"10.1186","volume":"12","author":[{"given":"Helen","family":"Gavillet","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauren","family":"Hatfield","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Jones","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anirban","family":"Maitra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Horsley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damian","family":"Rivett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"van der Gast","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,3,25]]},"reference":[{"key":"1780_CR1","doi-asserted-by":"publisher","first-page":"2519","DOI":"10.1016\/S0140-6736(16)00576-6","volume":"388","author":"JS Elborn","year":"2016","unstructured":"Elborn JS. Cystic fibrosis. Lancet. 2016;388:2519\u201331. https:\/\/doi.org\/10.1016\/S0140-6736(16)00576-6.","journal-title":"Lancet"},{"key":"1780_CR2","doi-asserted-by":"publisher","first-page":"S23","DOI":"10.1016\/j.jcf.2014.03.010","volume":"13","author":"AR Smyth","year":"2014","unstructured":"Smyth AR, Bell SC, Bojcin S, Bryon M, Duff A, Flume P, et al. European Cystic Fibrosis Society standards of care: best practice guidelines. J Cyst Fibros. 2014;13:S23\u201342. https:\/\/doi.org\/10.1016\/j.jcf.2014.03.010.","journal-title":"J Cyst Fibros"},{"key":"1780_CR3","doi-asserted-by":"publisher","first-page":"e00419","DOI":"10.1128\/spectrum.00419-22","volume":"10","author":"H Gavillet","year":"2022","unstructured":"Gavillet H, Hatfield L, Rivett D, Jones A, Maitra A, Horsley A, et al. Bacterial culture underestimates lung pathogen detection and infection status in cystic fibrosis. Microbiol Spectr. 2022;10:e00419-e422. https:\/\/doi.org\/10.1128\/spectrum.00419-22.","journal-title":"Microbiol Spectr"},{"key":"1780_CR4","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1016\/S1569-1993(02)00141-8","volume":"2","author":"TWR Lee","year":"2003","unstructured":"Lee TWR, Brownlee KG, Conway SP, Denton M, Littlewood JM. Evaluation of a new definition for chronic Pseudomonas aeruginosa infection in cystic fibrosis patients. J Cyst Fibros. 2003;2:29\u201334. https:\/\/doi.org\/10.1016\/S1569-1993(02)00141-8.","journal-title":"J Cyst Fibros"},{"key":"1780_CR5","doi-asserted-by":"publisher","first-page":"e00019","DOI":"10.1128\/CMR.00019-18","volume":"31","author":"MD Parkins","year":"2018","unstructured":"Parkins MD, Somayaji R, Waters VJ. Epidemiology, biology, and impact of clonal Pseudomonas aeruginosa infections in cystic fibrosis. Clin Microbiol Rev. 2018;31:e00019-e118. https:\/\/doi.org\/10.1128\/CMR.00019-18.","journal-title":"Clin Microbiol Rev"},{"key":"1780_CR6","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1016\/j.jcf.2009.11.009","volume":"9","author":"SJ Doe","year":"2010","unstructured":"Doe SJ, McSorley A, Isalska B, Kearns AM, Bright-Thomas R, Brennan AL, et al. Patient segregation and aggressive antibiotic eradication therapy can control methicillin-resistant Staphylococcus aureus at large cystic fibrosis centres. J Cyst Fibros. 2010;9:104\u20139. https:\/\/doi.org\/10.1016\/j.jcf.2009.11.009.","journal-title":"J Cyst Fibros"},{"key":"1780_CR7","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1186\/s40168-020-00810-3","volume":"8","author":"L Cuthbertson","year":"2020","unstructured":"Cuthbertson L, Walker AW, Oliver AE, Rogers GB, Rivett DW, Hampton TH, et al. Lung function and microbiota diversity in cystic fibrosis. Microbiome. 2020;8:45. https:\/\/doi.org\/10.1186\/s40168-020-00810-3.","journal-title":"Microbiome"},{"key":"1780_CR8","doi-asserted-by":"publisher","first-page":"e01763","DOI":"10.1128\/mBio.01763-21","volume":"12","author":"GA O\u2019Toole","year":"2021","unstructured":"O\u2019Toole GA, Crabb\u00e9 A, K\u00fcmmerli R, LiPuma JJ, Bomberger JM, Davies JC, et al. Model systems to study the chronic, polymicrobial infections in cystic fibrosis: current approaches and exploring future directions. mBio. 2021;12:e01763-21. https:\/\/doi.org\/10.1128\/mBio.01763-21.","journal-title":"mBio."},{"key":"1780_CR9","doi-asserted-by":"publisher","first-page":"e81604","DOI":"10.7554\/eLife.81604","volume":"12","author":"F Jean-Pierre","year":"2023","unstructured":"Jean-Pierre F, Hampton TH, Schultz D, Hogan DA, Groleau M-C, D\u00e9ziel E, et al. Community composition shapes microbial-specific phenotypes in a cystic fibrosis polymicrobial model system. eLife. 2023;12:e81604. https:\/\/doi.org\/10.7554\/eLife.81604.","journal-title":"eLife."},{"key":"1780_CR10","doi-asserted-by":"publisher","first-page":"e00292","DOI":"10.1128\/mSystems.00292-20","volume":"5","author":"R Raghuvanshi","year":"2020","unstructured":"Raghuvanshi R, Vasco K, V\u00e1zquez-Baeza Y, Jiang L, Morton James T, Li D, et al. High-resolution longitudinal dynamics of the cystic fibrosis sputum microbiome and metabolome through antibiotic therapy. mSystems. 2020;5:e00292-20. https:\/\/doi.org\/10.1128\/mSystems.00292-20.","journal-title":"mSystems."},{"key":"1780_CR11","doi-asserted-by":"publisher","first-page":"780","DOI":"10.1038\/ismej.2010.175","volume":"5","author":"CJ van der Gast","year":"2011","unstructured":"van der Gast CJ, Walker AW, Stressmann FA, Rogers GB, Scott P, Daniels TW, et al. Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities. ISME J. 2011;5:780\u201391. https:\/\/doi.org\/10.1038\/ismej.2010.175.","journal-title":"ISME J"},{"key":"1780_CR12","doi-asserted-by":"publisher","first-page":"00128","DOI":"10.1183\/23120541.00128-2017","volume":"5","author":"GG Einarsson","year":"2019","unstructured":"Einarsson GG, Zhao J, LiPuma JJ, Downey DG, Tunney MM, Elborn JS. Community analysis and co-occurrence patterns in airway microbial communities during health and disease. ERJ Open Res. 2019;5:00128\u20132017. https:\/\/doi.org\/10.1183\/23120541.00128-2017.","journal-title":"ERJ Open Res"},{"key":"1780_CR13","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1016\/S2213-2600(14)70028-1","volume":"2","author":"RP Dickson","year":"2014","unstructured":"Dickson RP, Erb-Downward JR, Huffnagle GB. Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis. Lancet Respir Med. 2014;2:238\u201346. https:\/\/doi.org\/10.1016\/S2213-2600(14)70028-1.","journal-title":"Lancet Respir Med"},{"key":"1780_CR14","doi-asserted-by":"publisher","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:e1004923. https:\/\/doi.org\/10.1371\/journal.ppat.1004923.","journal-title":"PLOS Pathog"},{"key":"1780_CR15","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/s41579-022-00821-x","volume":"21","author":"JG Natalini","year":"2023","unstructured":"Natalini JG, Singh S, Segal LN. The dynamic lung microbiome in health and disease. Nat Rev Microbiol. 2023;21:222\u201335. https:\/\/doi.org\/10.1038\/s41579-022-00821-x.","journal-title":"Nat Rev Microbiol"},{"key":"1780_CR16","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1164\/rccm.202112-2704PP","volume":"206","author":"SH Chotirmall","year":"2022","unstructured":"Chotirmall SH, Bogaert D, Chalmers JD, Cox MJ, Hansbro PM, Huang YJ, et al. Therapeutic targeting of the respiratory microbiome. Am J Respir Crit Care Med. 2022;206:535\u201344. https:\/\/doi.org\/10.1164\/rccm.202112-2704PP.","journal-title":"Am J Respir Crit Care Med"},{"key":"1780_CR17","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1038\/nrmicro1643","volume":"5","author":"JI Prosser","year":"2007","unstructured":"Prosser JI, Bohannan BJM, Curtis TP, Ellis RJ, Firestone MK, Freckleton RP, et al. The role of ecological theory in microbial ecology. Nat Rev Microbiol. 2007;5:384\u201392. https:\/\/doi.org\/10.1038\/nrmicro1643.","journal-title":"Nat Rev Microbiol"},{"key":"1780_CR18","doi-asserted-by":"publisher","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;189:1309\u201315. https:\/\/doi.org\/10.1164\/rccm.201312-2129PP.","journal-title":"Am J Respir Crit Care Med."},{"key":"1780_CR19","volume-title":"The theory of island biogeography","author":"RH MacArthur","year":"1967","unstructured":"MacArthur RH, Wilson EO. The theory of island biogeography. Princeton: Princeton University Press; 1967."},{"key":"1780_CR20","volume-title":"Measuring biological diversity","author":"AE Magurran","year":"2004","unstructured":"Magurran AE. Measuring biological diversity. Oxford: Blackwell Publishing; 2004."},{"key":"1780_CR21","doi-asserted-by":"publisher","first-page":"1884","DOI":"10.1126\/science.1111318","volume":"308","author":"T Bell","year":"2005","unstructured":"Bell T, Ager D, Song J-I, Newman JA, Thompson IP, Lilley AK, et al. Larger islands house more bacterial taxa. Science. 2005;308:1884. https:\/\/doi.org\/10.1126\/science.1111318.","journal-title":"Science."},{"key":"1780_CR22","doi-asserted-by":"publisher","first-page":"2947","DOI":"10.1038\/s41396-021-00976-0","volume":"15","author":"DW Rivett","year":"2021","unstructured":"Rivett DW, Mombrikotb SB, Gweon HS, Bell T, van der Gast C. Bacterial communities in larger islands have reduced temporal turnover. ISME J. 2021;15:2947\u201355. https:\/\/doi.org\/10.1038\/s41396-021-00976-0.","journal-title":"ISME J"},{"key":"1780_CR23","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1111\/1758-2229.12159","volume":"6","author":"AE Oliver","year":"2014","unstructured":"Oliver AE, Newbold LK, Whiteley AS, van der Gast CJ. Marine bacterial communities are resistant to elevated carbon dioxide levels. Environ Microbiol Rep. 2014;6:574\u201382. https:\/\/doi.org\/10.1111\/1758-2229.12159.","journal-title":"Environ Microbiol Rep"},{"key":"1780_CR24","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.1111\/j.1462-2920.2005.00802.x","volume":"7","author":"CJ van der Gast","year":"2005","unstructured":"van der Gast CJ, Lilley AK, Ager D, Thompson IP. Island size and bacterial diversity in an archipelago of engineering machines. Environ Microbiol. 2005;7:1220\u20136. https:\/\/doi.org\/10.1111\/j.1462-2920.2005.00802.x.","journal-title":"Environ Microbiol"},{"key":"1780_CR25","doi-asserted-by":"publisher","first-page":"1411","DOI":"10.1111\/j.1462-2920.2007.01550.x","volume":"10","author":"CJ van der Gast","year":"2008","unstructured":"van der Gast CJ, Ager D, Lilley AK. Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors. Environ Microbiol. 2008;10:1411\u20138. https:\/\/doi.org\/10.1111\/j.1462-2920.2007.01550.x.","journal-title":"Environ Microbiol"},{"key":"1780_CR26","doi-asserted-by":"publisher","first-page":"1048","DOI":"10.1111\/j.1462-2920.2006.00996.x","volume":"8","author":"CJ van der Gast","year":"2006","unstructured":"van der Gast CJ, Jefferson B, Reid E, Robinson T, Bailey MJ, Judd SJ, et al. Bacterial diversity is determined by volume in membrane bioreactors. Environ Microbiol. 2006;8:1048\u201355. https:\/\/doi.org\/10.1111\/j.1462-2920.2006.00996.x.","journal-title":"Environ Microbiol"},{"key":"1780_CR27","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1186\/s13059-014-0531-y","volume":"15","author":"GE Flores","year":"2014","unstructured":"Flores GE, Caporaso JG, Henley JB, Rideout JR, Domogala D, Chase J, et al. Temporal variability is a personalized feature of the human microbiome. Genome Biol. 2014;15:531. https:\/\/doi.org\/10.1186\/s13059-014-0531-y.","journal-title":"Genome Biol"},{"key":"1780_CR28","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1007\/s10096-017-3168-4","volume":"37","author":"ZH Hoo","year":"2018","unstructured":"Hoo ZH, Edenborough FP, Curley R, Prtak L, Dewar J, Allenby MI, et al. Understanding Pseudomonas status among adults with cystic fibrosis: a real-world comparison of the Leeds criteria against clinicians\u2019 decision. Eur J Clin Microbiol Infect Dis. 2018;37:735\u201343. https:\/\/doi.org\/10.1007\/s10096-017-3168-4.","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"1780_CR29","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1136\/thoraxjnl-2011-200932","volume":"67","author":"FA Stressmann","year":"2012","unstructured":"Stressmann FA, Rogers GB, van der Gast CJ, Marsh P, Vermeer LS, Carroll MP, et al. Long-term cultivation-independent microbial diversity analysis demonstrates that bacterial communities infecting the adult cystic fibrosis lung show stability and resilience. Thorax. 2012;67:867. https:\/\/doi.org\/10.1136\/thoraxjnl-2011-200932.","journal-title":"Thorax"},{"key":"1780_CR30","doi-asserted-by":"publisher","first-page":"1324","DOI":"10.1183\/09031936.00080312","volume":"40","author":"PH Quanjer","year":"2012","unstructured":"Quanjer PH, Stanojevic S, Cole TJ, Baur X, Hall GL, Culver BH, et al. Multi-ethnic reference values for spirometry for the 3\u201395-yr age range: the global lung function 2012 equations. Eur Respir J. 2012;40:1324. https:\/\/doi.org\/10.1183\/09031936.00080312.","journal-title":"Eur Respir J"},{"key":"1780_CR31","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1136\/thoraxjnl-2021-216928","volume":"77","author":"AR Horsley","year":"2022","unstructured":"Horsley AR, Belcher J, Bayfield K, Bianco B, Cunningham S, Fullwood C, et al. Longitudinal assessment of lung clearance index to monitor disease progression in children and adults with cystic fibrosis. Thorax. 2022;77:357. https:\/\/doi.org\/10.1136\/thoraxjnl-2021-216928.","journal-title":"Thorax"},{"key":"1780_CR32","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1016\/j.jcf.2014.10.004","volume":"14","author":"L Cuthbertson","year":"2015","unstructured":"Cuthbertson L, Rogers GB, Walker AW, Oliver A, Hoffman LR, Carroll MP, et al. Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses. J Cyst Fibros. 2015;14:464\u20137. https:\/\/doi.org\/10.1016\/j.jcf.2014.10.004.","journal-title":"J Cyst Fibros"},{"key":"1780_CR33","doi-asserted-by":"publisher","first-page":"3011","DOI":"10.1128\/JCM.00764-14","volume":"52","author":"L Cuthbertson","year":"2014","unstructured":"Cuthbertson L, Rogers Geraint B, Walker Alan W, Oliver A, Hafiz T, Hoffman Lucas R, et al. Time between collection and storage significantly influences bacterial sequence composition in sputum samples from cystic fibrosis respiratory infections. J Clin Microbiol. 2014;52:3011\u20136. https:\/\/doi.org\/10.1128\/JCM.00764-14.","journal-title":"J Clin Microbiol"},{"key":"1780_CR34","doi-asserted-by":"publisher","first-page":"3548","DOI":"10.1128\/JCM.41.8.3548-3558.2003","volume":"41","author":"GB Rogers","year":"2003","unstructured":"Rogers GB, Hart CA, Mason JR, Hughes M, Walshaw MJ, Bruce KD. Bacterial diversity in cases of lung infection in cystic fibrosis patients: 16S ribosomal DNA (rDNA) length heterogeneity PCR and 16S rDNA terminal restriction fragment length polymorphism profiling. J Clin Microbiol. 2003;41:3548\u201358. https:\/\/doi.org\/10.1128\/JCM.41.8.3548-3558.2003.","journal-title":"J Clin Microbiol"},{"key":"1780_CR35","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2023.03.008","author":"L Hatfield","year":"2023","unstructured":"Hatfield L, Bianco B, Gavillet H, Burns P, Rivett D, Smith M, et al. Effects of postage on recovery of pathogens from cystic fibrosis sputum samples. J Cyst Fibros. 2023. https:\/\/doi.org\/10.1016\/j.jcf.2023.03.008.","journal-title":"J Cyst Fibros"},{"key":"1780_CR36","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1016\/j.jcf.2021.11.014","volume":"21","author":"R Marsh","year":"2022","unstructured":"Marsh R, Gavillet H, Hanson L, Ng C, Mitchell-Whyte M, Major G, et al. Intestinal function and transit associate with gut microbiota dysbiosis in cystic fibrosis. J Cyst Fibros. 2022;21:506\u201313. https:\/\/doi.org\/10.1016\/j.jcf.2021.11.014.","journal-title":"J Cyst Fibros"},{"key":"1780_CR37","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","volume":"36","author":"P-A Chaumeil","year":"2020","unstructured":"Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics. 2020;36:1925\u20137. https:\/\/doi.org\/10.1093\/bioinformatics\/btz848.","journal-title":"Bioinformatics"},{"key":"1780_CR38","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403\u201310. https:\/\/doi.org\/10.1016\/S0022-2836(05)80360-2.","journal-title":"J Mol Biol"},{"key":"1780_CR39","doi-asserted-by":"publisher","first-page":"714","DOI":"10.1038\/nature01547","volume":"422","author":"AE Magurran","year":"2003","unstructured":"Magurran AE, Henderson PA. Explaining the excess of rare species in natural species abundance distributions. Nature. 2003;422:714\u20136. https:\/\/doi.org\/10.1038\/nature01547.","journal-title":"Nature"},{"key":"1780_CR40","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1086\/652373","volume":"85","author":"M Vellend","year":"2010","unstructured":"Vellend M. Conceptual synthesis in community ecology. Q Rev Biol. 2010;85:183\u2013206. https:\/\/doi.org\/10.1086\/652373.","journal-title":"Q Rev Biol"},{"key":"1780_CR41","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1890\/ES10-00117.1","volume":"2","author":"JM Chase","year":"2011","unstructured":"Chase JM, Kraft NJB, Smith KG, Vellend M, Inouye BD. Using null models to disentangle variation in community dissimilarity from variation in \u03b1-diversity. Ecosphere. 2011;2:24. https:\/\/doi.org\/10.1890\/ES10-00117.1.","journal-title":"Ecosphere"},{"key":"1780_CR42","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1128\/MMBR.00051-12","volume":"77","author":"DR Nemergut","year":"2013","unstructured":"Nemergut DR, Schmidt SK, Fukami T, O\u2019Neill SP, Bilinski TM, Stanish LF, et al. Patterns and processes of microbial community assembly. Microbiol Mol Biol Rev. 2013;77:342\u201356. https:\/\/doi.org\/10.1128\/MMBR.00051-12.","journal-title":"Microbiol Mol Biol Rev"},{"key":"1780_CR43","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2022.07.009","author":"DA Hughes","year":"2022","unstructured":"Hughes DA, Rosenthal M, Cuthbertson L, Ramadan N, Felton I, Simmonds NJ, et al. An invisible threat? Aspergillus positive cultures and co-infecting bacteria in airway samples. J Cyst Fibros. 2022. https:\/\/doi.org\/10.1016\/j.jcf.2022.07.009.","journal-title":"J Cyst Fibros"},{"key":"1780_CR44","doi-asserted-by":"publisher","first-page":"888","DOI":"10.1016\/j.jcf.2022.04.017","volume":"21","author":"CF Zirbes","year":"2022","unstructured":"Zirbes CF, Pitcher NJ, Davis JC, Bartels AR, Krogh JD, Teresi M, et al. Staphylococcus aureus detection from CF respiratory samples is improved using alternative media. J Cyst Fibros. 2022;21:888\u20139. https:\/\/doi.org\/10.1016\/j.jcf.2022.04.017.","journal-title":"J Cyst Fibros"},{"key":"1780_CR45","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1038\/ismej.2014.124","volume":"9","author":"GB Rogers","year":"2015","unstructured":"Rogers GB, van der Gast CJ, Serisier DJ. Predominant pathogen competition and core microbiota divergence in chronic airway infection. ISME J. 2015;9:217\u201325. https:\/\/doi.org\/10.1038\/ismej.2014.124.","journal-title":"ISME J"},{"key":"1780_CR46","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1513\/AnnalsATS.201501-029OC","volume":"12","author":"RP Dickson","year":"2015","unstructured":"Dickson RP, Erb-Downward JR, Freeman CM, McCloskey L, Beck JM, Huffnagle GB, et al. Spatial variation in the healthy human lung microbiome and the adapted island model of lung biogeography. Ann Am Thorac Soc. 2015;12:821\u201330. https:\/\/doi.org\/10.1513\/AnnalsATS.201501-029OC.","journal-title":"Ann Am Thorac Soc"},{"key":"1780_CR47","doi-asserted-by":"publisher","first-page":"1493","DOI":"10.1038\/ismej.2013.54","volume":"7","author":"A Shade","year":"2013","unstructured":"Shade A, Gregory Caporaso J, Handelsman J, Knight R, Fierer N. A meta-analysis of changes in bacterial and archaeal communities with time. ISME J. 2013;7:1493\u2013506. https:\/\/doi.org\/10.1038\/ismej.2013.54.","journal-title":"ISME J"},{"key":"1780_CR48","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1111\/j.0030-1299.2006.14223.x","volume":"112","author":"EP White","year":"2006","unstructured":"White EP, Adler P, Lauenroth WK, Gill RA, Greenberg D, Kaufman DM, et al. A comparison of the species\u2013time relationship across ecosystems and taxonomic groups. Oikos. 2006;112:185\u201395. https:\/\/doi.org\/10.1111\/j.0030-1299.2006.14223.x.","journal-title":"Oikos"},{"key":"1780_CR49","doi-asserted-by":"publisher","first-page":"e01371","DOI":"10.1128\/mBio.01371-14","volume":"5","author":"A Shade","year":"2014","unstructured":"Shade A, Jones Stuart E, Caporaso JG, Handelsman J, Knight R, Fierer N, et al. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio. 2014;5:e01371-14. https:\/\/doi.org\/10.1128\/mBio.01371-14.","journal-title":"mBio."},{"key":"1780_CR50","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1007\/BF02914538","volume":"9","author":"M Berger","year":"1991","unstructured":"Berger M. Inflammation in the lung in cystic fibrosis. A vicious cycle that does more harm than good? Clin Rev Allergy. 1991;9:119\u201342. https:\/\/doi.org\/10.1007\/BF02914538.","journal-title":"Clin Rev Allergy."},{"key":"1780_CR51","doi-asserted-by":"publisher","first-page":"2069","DOI":"10.1038\/ismej.2013.93","volume":"7","author":"JC Stegen","year":"2013","unstructured":"Stegen JC, Lin X, Fredrickson JK, Chen X, Kennedy DW, Murray CJ, et al. Quantifying community assembly processes and identifying features that impose them. ISME J. 2013;7:2069\u201379. https:\/\/doi.org\/10.1038\/ismej.2013.93.","journal-title":"ISME J"}],"container-title":["Microbiome"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-024-01780-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s40168-024-01780-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-024-01780-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,25]],"date-time":"2024-03-25T05:12:36Z","timestamp":1711343556000},"score":1,"resource":{"primary":{"URL":"https:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-024-01780-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,25]]},"references-count":51,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["1780"],"URL":"https:\/\/doi.org\/10.1186\/s40168-024-01780-6","relation":{},"ISSN":["2049-2618"],"issn-type":[{"value":"2049-2618","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,3,25]]},"assertion":[{"value":"10 July 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 February 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 March 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Patients or parents\/guardians provided written informed consent and children provided assent. This study was reviewed and approved by the NHS Research Ethics Committee North-West, Lancaster (Ref 14\/NW\/1195).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"Outside of the submitted work, CvdG and DR report grants from Vertex Pharmaceuticals, and AH reports personal fees for advisory services (Vertex Pharmaceuticals, Roche Genentech, Boehringer Ingelheim) and for educational and presentation activities (Vertex Pharmaceuticals)","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"63"}}