{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T13:49:13Z","timestamp":1792158553684,"version":"4.4.0"},"reference-count":78,"publisher":"American Society for Microbiology","license":[{"start":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T00:00:00Z","timestamp":1792108800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T00:00:00Z","timestamp":1792108800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["182499 and 212266"],"award-info":[{"award-number":["182499 and 212266"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UZH Research Priority Program (URPP) - Evolition in Action"},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/M01116X\/1"],"award-info":[{"award-number":["BB\/M01116X\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Polymicrobial airway colonization is common in individuals with cystic fibrosis (CF). Pathogen communities typically follow an ecological succession in which early colonizers, such as\n                      <jats:italic toggle=\"yes\">Haemophilus influenzae<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">Staphylococcus aureus,<\/jats:italic>\n                      are later joined by\n                      <jats:italic toggle=\"yes\">Pseudomonas aeruginosa<\/jats:italic>\n                      . Although adaptation to the lung environment is well described for single pathogens in adult people with CF, much less is known about the role of pathogen interactions and how changes in individual pathogens influence community dynamics at the early stages of disease. To address these questions, we combined genome sequencing with phenotypic screens and pathogen interaction assays using longitudinal clinical isolates (19\n                      <jats:italic toggle=\"yes\">P. aeruginosa<\/jats:italic>\n                      , 44\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      , and 21\n                      <jats:italic toggle=\"yes\">H. influenzae<\/jats:italic>\n                      ) collected from 23 children with CF (0\u20137.9 years of age) enrolled in the Swiss Cystic Fibrosis Infant Lung Development (SCILD) cohort. Our analysis suggests that early pathogen communities are characterized by a combination of strain turnover and persistence of specific isolates that go along with cohort-wide, age-associated shifts in pathogen phenotypes and interaction patterns. Most notably, quorum-sensing-deficient\n                      <jats:italic toggle=\"yes\">P. aeruginosa<\/jats:italic>\n                      variants repeatedly emerged, showing reduced protease production and diminished inhibition of\n                      <jats:italic toggle=\"yes\">S. aureus<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">H. influenzae<\/jats:italic>\n                      . These changes demonstrate that\n                      <jats:italic toggle=\"yes\">P. aeruginosa<\/jats:italic>\n                      isolates from older children exhibit reduced antagonism toward co-occurring pathogens via secreted factors. Together, our results show that ecological and evolutionary dynamics between pathobiome members may play an underappreciated role in shaping CF lung disease during early childhood.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Our study shows how bacterial communities in the lungs of children with cystic fibrosis change during the earliest stages of disease. By tracking three major pathogens over time, we found that both replacement of strains and persistence shape colonization dynamics and pathogen interaction patterns. In particular,\n                      <jats:italic toggle=\"yes\">Pseudomonas aeruginosa<\/jats:italic>\n                      frequently showed mutations that reduced its production of harmful compounds and weakened its ability to inhibit other bacteria. These changes indicate that interspecies interactions are dynamic during early childhood. Understanding these early interaction patterns provides useful cues about potential future microbial management in cystic fibrosis.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01577-26","type":"journal-article","created":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T13:00:56Z","timestamp":1792155656000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Tracking eco-evolutionary patterns among oropharyngeal pathobiome members in a pediatric cystic fibrosis cohort"],"prefix":"10.1128","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2063-6404","authenticated-orcid":true,"given":"Lukas","family":"Schwyter","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02crff812","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Quantitative Biomedicine, University of Zurich","place":["Zurich, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roger","family":"Kuratli","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02crff812","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Quantitative Biomedicine, University of Zurich","place":["Zurich, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Serena","family":"Provveduto","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02crff812","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Quantitative Biomedicine, University of Zurich","place":["Zurich, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phoebe","family":"Do Carmo Silva","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01a77tt86","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Life Sciences, University of Warwick","place":["Coventry, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philipp","family":"Latzin","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02k7v4d05","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Pediatric Respiratory Medicine and Allergology, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern","place":["Bern, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Freya","family":"Harrison","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01a77tt86","id-type":"ROR","asserted-by":"publisher"}],"name":"School of Life Sciences, University of Warwick","place":["Coventry, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"Hilty","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02k7v4d05","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute for Infectious Diseases, University of Bern","place":["Bern, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4084-6679","authenticated-orcid":true,"given":"Rolf","family":"K\u00fcmmerli","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02crff812","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Quantitative Biomedicine, University of Zurich","place":["Zurich, Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","published-online":{"date-parts":[[2026,10,16]]},"reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00809-20"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1006798"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1005846"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00036-10"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1005258"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep10241"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.15.2.194-222.2002"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1569-1993(11)60011-8"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1097\/MCP.0000000000000616"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens3030680"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0024301"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng.997"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3148"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2016.01.008"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1093\/jpids\/piac073"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.adi0908"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00755-09"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1018249108"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000513"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0602138103"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1508324112"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.81604"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2019.06.004"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1183\/20734735.014718"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00962-20"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.03153-22"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.4414\/smw.2018.14618"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004651"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.278.5338.631"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.33"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.42.2.792-799.2004"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00724-23"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-19240-2"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/143.4.517"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01968-05"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmm.2011.08.003"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1810840115"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2024.1374466"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00335-07"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.38.12.4649-4652.2000"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-00509-4"},{"key":"e_1_3_4_43_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.926758"},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.00174-22"},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-52726-0"},{"key":"e_1_3_4_46_2","doi-asserted-by":"publisher","DOI":"10.3791\/67213"},{"key":"e_1_3_4_47_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01395-09"},{"key":"e_1_3_4_48_2","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00354-22"},{"key":"e_1_3_4_49_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2007.05678.x"},{"key":"e_1_3_4_50_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(16)00576-6"},{"key":"e_1_3_4_51_2","doi-asserted-by":"publisher","DOI":"10.1136\/archdischild-2013-304400"},{"key":"e_1_3_4_52_2","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics10070827"},{"key":"e_1_3_4_53_2","doi-asserted-by":"publisher","DOI":"10.1186\/s40348-016-0067-1"},{"key":"e_1_3_4_54_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01513-16"},{"key":"e_1_3_4_55_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1819796116"},{"key":"e_1_3_4_56_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01592-14"},{"key":"e_1_3_4_57_2","doi-asserted-by":"publisher","DOI":"10.1172\/JCI6277"},{"key":"e_1_3_4_58_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms24044052"},{"key":"e_1_3_4_59_2","doi-asserted-by":"publisher","DOI":"10.1164\/rccm.201009-1430OC"},{"key":"e_1_3_4_60_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0705653104"},{"key":"e_1_3_4_61_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01211-09"},{"key":"e_1_3_4_62_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkt072"},{"key":"e_1_3_4_63_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12890-023-02611-4"},{"key":"e_1_3_4_64_2","doi-asserted-by":"publisher","DOI":"10.1183\/09031936.00204411"},{"key":"e_1_3_4_65_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_3_4_66_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_3_4_67_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"e_1_3_4_68_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv421"},{"key":"e_1_3_4_69_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1832-y"},{"key":"e_1_3_4_70_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0721-2"},{"key":"e_1_3_4_71_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009490"},{"key":"e_1_3_4_72_2","doi-asserted-by":"publisher","unstructured":"Emms DM Kelly S. 2018. STAG: species tree inference from all genes. bioRxiv. doi:10.1101\/267914","DOI":"10.1101\/267914"},{"key":"e_1_3_4_73_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx259"},{"key":"e_1_3_4_74_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msab293"},{"key":"e_1_3_4_75_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki008"},{"key":"e_1_3_4_76_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0167-4838(00)00018-2"},{"key":"e_1_3_4_77_2","doi-asserted-by":"publisher","DOI":"10.1016\/0003-2697(87)90612-9"},{"key":"e_1_3_4_78_2","doi-asserted-by":"publisher","DOI":"10.1002\/evl3.144"},{"key":"e_1_3_4_79_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00284-006-0601-9"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01577-26","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01577-26","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T13:00:57Z","timestamp":1792155657000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.01577-26"}},"subtitle":[],"editor":[{"given":"Jianmin","family":"Chai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,10,16]]},"references-count":78,"alternative-id":["10.1128\/spectrum.01577-26"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.01577-26","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,16]]},"assertion":[{"value":"2026-05-18","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-23","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-10-16","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01577-26"}}