{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T13:18:56Z","timestamp":1789996736374,"version":"4.0.1"},"reference-count":82,"publisher":"American Society for Microbiology","issue":"9","license":[{"start":{"date-parts":[[2025,9,2]],"date-time":"2025-09-02T00:00:00Z","timestamp":1756771200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,9,2]],"date-time":"2025-09-02T00:00:00Z","timestamp":1756771200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100000292","name":"Cystic Fibrosis Trust","doi-asserted-by":"publisher","award":["VIA078"],"award-info":[{"award-number":["VIA078"]}],"id":[{"id":"10.13039\/501100000292","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001308","name":"Jean Shanks Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001308","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,9,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Nontuberculous mycobacterial (NTM) infections in people with cystic fibrosis (pwCF) can have detrimental effects on prognosis and pose significant challenges to treatment. However, there are still questions regarding the contribution and influence of NTMs on the respiratory microbiome and the mechanisms by which NTMs cause infections. Here, we investigate the impact of NTM infection on microbiome composition and lung function (percent predicted forced expiratory volume in 1 second). Primary comparisons were between culture-positive cohorts for\n                      <jats:italic toggle=\"yes\">Mycobacterium avium<\/jats:italic>\n                      complex and\n                      <jats:italic toggle=\"yes\">Mycobacterium abscessus<\/jats:italic>\n                      complex and those who were culture-negative for NTMs and attending outpatient clinics. Additionally, the consequence of cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy status and positive NTM culture was assessed in terms of microbiome change. Our data suggest that the presence of NTM significantly alters the diversity and the composition of the lung microbiota in pwCF, including those receiving CFTR modulator therapies. Importantly, significant associations were detected between NTM presence and changes in abundance of\n                      <jats:italic toggle=\"yes\">Pseudomonas aeruginosa<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">Burkholderia cepacia<\/jats:italic>\n                      complex members, inferring modulatory effects of NTMs on respiratory microbiomes. This study contributes to the understanding of NTM infection and these organisms\u2019 interaction with the respiratory microbiome and CFTR modulator therapy, highlighting the need for further research in this area.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        The influence of NTM infection in pwCF is still debated, and the extent of their contribution to mortality and morbidity is still questioned. Findings in this study highlight a link between the presence of NTMs and significant alterations in the composition of the respiratory microbiome, particularly with respect to some of the canonical CF pathogens, especially\n                        <jats:italic toggle=\"yes\">Pseudomonas aeruginosa<\/jats:italic>\n                        and members of the\n                        <jats:italic toggle=\"yes\">Burkholderia cepacia<\/jats:italic>\n                        complex. This indicates that complex relationships are occurring within the microbiome. This study further contributes to the understanding of NTM infection in pwCF, with and without CFTR modulator therapy, and highlights the need for further research in this area. The knowledge gained from this study has implications for treatment strategies and management, ultimately aiming to improve and prolong the lives of pwCF.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.00382-25","type":"journal-article","created":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T02:00:42Z","timestamp":1754013642000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":4,"title":["Nontuberculous mycobacteria remodel lung microbiota in cystic fibrosis-associated respiratory infections"],"prefix":"10.1128","volume":"13","author":[{"given":"Michelle","family":"Hardman","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/009ec3j55","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Life Sciences, Manchester Metropolitan University","place":["Manchester, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Higgi","sequence":"additional","affiliation":[{"name":"The Grange University Hospital","place":["Cwmbran, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liam","family":"Hanson","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/009ec3j55","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Life Sciences, Manchester Metropolitan University","place":["Manchester, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristin","family":"Schutz","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0155zta11","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont","place":["Burlington, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew J.","family":"Wargo","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0155zta11","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology and Molecular Genetics, Larner College of Medicine, University of Vermont","place":["Burlington, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlotte C.","family":"Teneback","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0155zta11","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Pulmonary and Critic, Care Medicine, Department of Medicine, Larner College of Medicine, University of Vermont","place":["Burlington, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas W. V.","family":"Daniels","sequence":"additional","affiliation":[{"name":"Wessex Adult Cystic Fibrosis Unit, University Hospitals Southampton NHS Foundation Trust","place":["Southampton, United Kingdom"]},{"id":[{"id":"https:\/\/ror.org\/01qqpzg67","id-type":"ROR","asserted-by":"publisher"}],"name":"National Institute for Health Research, Southampton Biomedical Research Centre","place":["Southampton, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1101-4048","authenticated-orcid":true,"given":"Christopher","family":"van der Gast","sequence":"additional","affiliation":[{"name":"Department of Applied Sciences, Northumbria University","place":["Newcastle, United Kingdom"]},{"name":"Department of Respiratory Medicine, Northern Care Alliance NHS Foundation Trust","place":["Salford, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1852-6137","authenticated-orcid":true,"given":"Damian W.","family":"Rivett","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/009ec3j55","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Natural Sciences, Manchester Metropolitan University","place":["Manchester, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","unstructured":"The Cystic Fibrosis Trust. 2019. What is cystic fibrosis? Available from: https:\/\/www.cysticfibrosis.org.uk\/what-is-cystic-fibrosis. Accessed 10 Sep 2019."},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.2475911"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(16)00576-6"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1002\/cbic.201500620"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1183\/16000617.0068-2024"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1136\/thoraxjnl-2015-207360"},{"key":"e_1_3_5_8_2","unstructured":"National Jewish Health. 2023. Cystic fibrosis: life expectancy. Available from: https:\/\/www.nationaljewish.org\/conditions\/cystic-fibrosis-cf\/life-expectancy. Retrieved 24 Apr 2023."},{"key":"e_1_3_5_9_2","volume-title":"Mycobacterium abcessus: recommendations for infection prevention and control","author":"The Cystic Fibrosis Trust","year":"2017","unstructured":"The Cystic Fibrosis Trust. 2017. Mycobacterium abcessus: recommendations for infection prevention and control. The CF trust."},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1007\/s40506-016-0092-6"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1513\/AnnalsATS.201309-310OC"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.1183\/23120541.00578-2020"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.healun.2021.07.005"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2023.08.035"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.3201\/2109.141634"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.200604-571ST"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1055\/s-0033-1333568"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.1136\/thoraxjnl-2017-210927"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2015.09.007"},{"key":"e_1_3_5_20_2","article-title":"Nontuberculous mycobacteria 1: multicenter prevalence study in cystic fibrosis","author":"Olivier KN","year":"2012","unstructured":"Olivier KN, Weber DJ, Wallace RJ, et al.. 2012. Nontuberculous mycobacteria 1: multicenter prevalence study in cystic fibrosis. Am J Respir Crit Care Med. doi:http:\/\/dxdoiorg\/101164\/rccm200207-678OC","journal-title":"Am J Respir Crit Care Med"},{"key":"e_1_3_5_21_2","doi-asserted-by":"publisher","DOI":"10.1136\/bmjresp-2020-000591"},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-37350-8"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.1183\/23120541.00336-2022"},{"key":"e_1_3_5_24_2","doi-asserted-by":"publisher","DOI":"10.1513\/AnnalsATS.201709-727OC"},{"key":"e_1_3_5_25_2","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciy531"},{"key":"e_1_3_5_26_2","volume-title":"The cystic fibrosis trust","author":"Sokhi S","year":"2021","unstructured":"Sokhi S, Charrman S, Carr S, et al.. 2021. UK cystic fibrosis registry, 2021 annual data report. In The cystic fibrosis trust. Online."},{"key":"e_1_3_5_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccm.2014.10.002"},{"key":"e_1_3_5_28_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2908.230378"},{"key":"e_1_3_5_29_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jctube.2021.100271"},{"key":"e_1_3_5_30_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0011007"},{"key":"e_1_3_5_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02282-05"},{"key":"e_1_3_5_32_2","doi-asserted-by":"publisher","DOI":"10.1155\/2012\/746358"},{"key":"e_1_3_5_33_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-020-00810-3"},{"key":"e_1_3_5_34_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-024-01780-6"},{"key":"e_1_3_5_35_2","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.01456-24"},{"key":"e_1_3_5_36_2","doi-asserted-by":"publisher","DOI":"10.3402\/jom.v7.26094"},{"key":"e_1_3_5_37_2","doi-asserted-by":"publisher","DOI":"10.1111\/resp.12536"},{"key":"e_1_3_5_38_2","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.00810-2018"},{"key":"e_1_3_5_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2023.05.003"},{"key":"e_1_3_5_40_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3869"},{"key":"e_1_3_5_41_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00764-14"},{"key":"e_1_3_5_42_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2023.03.008"},{"key":"e_1_3_5_43_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2021.08.031"},{"key":"e_1_3_5_44_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12931-023-02630-z"},{"key":"e_1_3_5_45_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2021.11.003"},{"key":"e_1_3_5_46_2","doi-asserted-by":"publisher","DOI":"10.1136\/thorax-2022-219943"},{"key":"e_1_3_5_47_2","doi-asserted-by":"publisher","DOI":"10.1136\/thoraxjnl-2012-202018"},{"key":"e_1_3_5_48_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2021.763121"},{"key":"e_1_3_5_49_2","doi-asserted-by":"publisher","DOI":"10.1513\/AnnalsATS.201211-107OC"},{"key":"e_1_3_5_50_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chest.2016.06.005"},{"key":"e_1_3_5_51_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcf.2014.12.002"},{"key":"e_1_3_5_52_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12890-017-0544-x"},{"key":"e_1_3_5_53_2","doi-asserted-by":"publisher","DOI":"10.1080\/14656566.2021.1953472"},{"key":"e_1_3_5_54_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003057"},{"key":"e_1_3_5_55_2","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201609-1954OC"},{"key":"e_1_3_5_56_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.syapm.2010.10.002"},{"key":"e_1_3_5_57_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.01592"},{"key":"e_1_3_5_58_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00029-16"},{"key":"e_1_3_5_59_2","doi-asserted-by":"publisher","DOI":"10.1172\/JCI167957"},{"key":"e_1_3_5_60_2","volume-title":"UK cystic fibrosis registry 2023 annual data report","author":"Cystic Fibrosis Trust","year":"2024","unstructured":"Cystic Fibrosis Trust. 2024. UK cystic fibrosis registry 2023 annual data report. Cystic Fibrosis Trust, London."},{"key":"e_1_3_5_61_2","volume-title":"2023 annual data report","author":"Cystic Fibrosis Foundation Patient Registry","year":"2023","unstructured":"Cystic Fibrosis Foundation Patient Registry. 2023. 2023 annual data report. Cystic Fibrosis Foundation, Bethesda, Maryland."},{"key":"e_1_3_5_62_2","doi-asserted-by":"publisher","DOI":"10.1136\/thorax-2023-220100"},{"key":"e_1_3_5_63_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-13036-1"},{"key":"e_1_3_5_64_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks808"},{"key":"e_1_3_5_65_2","doi-asserted-by":"publisher","DOI":"10.3343\/kjlm.2006.26.3.153"},{"key":"e_1_3_5_66_2","doi-asserted-by":"publisher","DOI":"10.1590\/0074-02760220031"},{"key":"e_1_3_5_67_2","doi-asserted-by":"publisher","DOI":"10.1128\/cmr.17.4.840-862.2004"},{"key":"e_1_3_5_68_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1569-1993(02)00141-8"},{"key":"e_1_3_5_69_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.02987-06"},{"key":"e_1_3_5_70_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2012.145"},{"key":"e_1_3_5_71_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.diagmicrobio.2008.06.011"},{"key":"e_1_3_5_72_2","doi-asserted-by":"publisher","DOI":"10.1101\/2020.06.05.134197"},{"key":"e_1_3_5_73_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-015-0450-4"},{"key":"e_1_3_5_74_2","doi-asserted-by":"publisher","DOI":"10.1002\/iub.1969"},{"key":"e_1_3_5_75_2","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201210-1913OC"},{"key":"e_1_3_5_76_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0016384"},{"key":"e_1_3_5_77_2","unstructured":"R Core Team. 2023. R: a language and environment for statistical computing. Available from: https:\/\/www.R-project.org"},{"key":"e_1_3_5_78_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1219"},{"key":"e_1_3_5_79_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1990.9999"},{"key":"e_1_3_5_80_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab1112"},{"key":"e_1_3_5_81_2","doi-asserted-by":"publisher","DOI":"10.1890\/08-1823.1"},{"key":"e_1_3_5_82_2","volume-title":"An R companion to applied regression","author":"Fox J","year":"2019","unstructured":"Fox J, Weisberg S. 2019. An R companion to applied regression. 3rd. Sage, Thousand Oaks, CA.","edition":"3"},{"key":"e_1_3_5_83_2","unstructured":"Oksanen JB Guillaume F Friendly M Kindt R Legendre P McGlinn D Peter R. M O\u2019Hara RB Gavin L. S Solymos P M. Henry HS Szoecs E Helene W. 2025 Helene Vegan: Community Ecology Package. Available from: http:\/\/CRANR-projectorg\/package=vegan2016"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.00382-25","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.00382-25","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,2]],"date-time":"2025-09-02T13:05:56Z","timestamp":1756818356000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.00382-25"}},"subtitle":[],"editor":[{"given":"Silvia T.","family":"Cardona","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,9,2]]},"references-count":82,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2025,9,2]]}},"alternative-id":["10.1128\/spectrum.00382-25"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.00382-25","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,2]]},"assertion":[{"value":"2025-02-13","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-06-29","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-07-31","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00382-25"}}