{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T00:39:35Z","timestamp":1792715975182,"version":"4.5.0"},"reference-count":89,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T00:00:00Z","timestamp":1782950400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T00:00:00Z","timestamp":1792713600000},"content-version":"vor","delay-in-days":113,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"Wuhan Health Commission","award":["WX23A90"],"award-info":[{"award-number":["WX23A90"]}]},{"name":"Wuhan Health Commission","award":["WX23A90"],"award-info":[{"award-number":["WX23A90"]}]},{"DOI":"10.13039\/501100003819","name":"Natural Science Foundation of Hubei Province","doi-asserted-by":"publisher","award":["2023AFB221, 2021CFA012"],"award-info":[{"award-number":["2023AFB221, 2021CFA012"]}],"id":[{"id":"10.13039\/501100003819","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003819","name":"Natural Science Foundation of Hubei Province","doi-asserted-by":"publisher","award":["2023AFB221, 2021CFA012"],"award-info":[{"award-number":["2023AFB221, 2021CFA012"]}],"id":[{"id":"10.13039\/501100003819","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003819","name":"Natural Science Foundation of Hubei Province","doi-asserted-by":"publisher","award":["2023AFB221, 2021CFA012"],"award-info":[{"award-number":["2023AFB221, 2021CFA012"]}],"id":[{"id":"10.13039\/501100003819","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003819","name":"Natural Science Foundation of Hubei Province","doi-asserted-by":"publisher","award":["2023AFB221, 2021CFA012"],"award-info":[{"award-number":["2023AFB221, 2021CFA012"]}],"id":[{"id":"10.13039\/501100003819","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Wuhan Children's Hospital","award":["2024FEBSJJ007"],"award-info":[{"award-number":["2024FEBSJJ007"]}]},{"name":"Wuhan Children's Hospital","award":["2024FEBSJJ007"],"award-info":[{"award-number":["2024FEBSJJ007"]}]},{"DOI":"10.13039\/100017958","name":"Health Commission of Hubei Province","doi-asserted-by":"publisher","award":["WJ2021M262"],"award-info":[{"award-number":["WJ2021M262"]}],"id":[{"id":"10.13039\/100017958","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017958","name":"Health Commission of Hubei Province","doi-asserted-by":"publisher","award":["WJ2021M262"],"award-info":[{"award-number":["WJ2021M262"]}],"id":[{"id":"10.13039\/100017958","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017958","name":"Health Commission of Hubei Province","doi-asserted-by":"publisher","award":["WJ2021M262"],"award-info":[{"award-number":["WJ2021M262"]}],"id":[{"id":"10.13039\/100017958","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017958","name":"Health Commission of Hubei Province","doi-asserted-by":"publisher","award":["WJ2021M262"],"award-info":[{"award-number":["WJ2021M262"]}],"id":[{"id":"10.13039\/100017958","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["npj Biofilms Microbiomes"],"DOI":"10.1038\/s41522-026-01075-8","type":"journal-article","created":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T12:25:51Z","timestamp":1782995151000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Pharyngeal Microenvironment Associated with Human Rhinovirus Infection in Children: Insights from Metatranscriptomic Sequencing"],"prefix":"10.1038","volume":"12","author":[{"given":"Muhammad","family":"Noman","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaming","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haizhou","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ismaila","family":"Damilare Isiaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Arif","family":"Rizwan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hebin","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenqing","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanli","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiali","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueru","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Du","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Youjing","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qing","family":"Du","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Di","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoxia","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Yan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,2]]},"reference":[{"key":"1075_CR1","doi-asserted-by":"publisher","first-page":"1204","DOI":"10.1016\/S0140-6736(20)30925-9","volume":"396","author":"T Vos","year":"2020","unstructured":"Vos, T. et al. Global burden of 369 diseases and injuries in 204 countries and territories, 1990\u20132019: a systematic analysis for the Global Burden of Disease Study 2019. lancet 396, 1204\u20131222 (2020).","journal-title":"lancet"},{"key":"1075_CR2","unstructured":"Organization, W. H. The top 10 causes of death. (2024)."},{"key":"1075_CR3","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/S2213-2600(18)30496-X","volume":"7","author":"CE Troeger","year":"2019","unstructured":"Troeger, C. E. et al. Mortality, morbidity, and hospitalisations due to influenza lower respiratory tract infections, 2017: an analysis for the Global Burden of Disease Study 2017. Lancet Resp. Med. 7, 69\u201389 (2019).","journal-title":"Lancet Resp. Med."},{"key":"1075_CR4","unstructured":"Knipe, D. M. & Howley, P. Fields Virology (Wolters Kluwer Health, 2013)."},{"key":"1075_CR5","doi-asserted-by":"publisher","first-page":"293","DOI":"10.3389\/fmicb.2013.00293","volume":"4","author":"D Kurai","year":"2013","unstructured":"Kurai, D., Saraya, T., Ishii, H. & Takizawa, H. Virus-induced exacerbations in asthma and COPD. Front. Microbiol. 4, 293 (2013).","journal-title":"Front. Microbiol."},{"key":"1075_CR6","doi-asserted-by":"publisher","first-page":"1886","DOI":"10.3201\/eid1811.120607","volume":"18","author":"VTN Bich","year":"2012","unstructured":"Bich, V. T. N. et al. Fatal respiratory infections associated with rhinovirus outbreak, Vietnam. Emerg. Infect. Dis. 18, 1886 (2012).","journal-title":"Emerg. Infect. Dis."},{"key":"1075_CR7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.jcv.2014.12.021","volume":"64","author":"J Ambrosioni","year":"2015","unstructured":"Ambrosioni, J. et al. Role of rhinovirus load in the upper respiratory tract and severity of symptoms in lung transplant recipients. J. Clin. Virol. 64, 1\u20135 (2015).","journal-title":"J. Clin. Virol."},{"key":"1075_CR8","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1056\/NEJMoa1500245","volume":"373","author":"S Jain","year":"2015","unstructured":"Jain, S. et al. Community-acquired pneumonia requiring hospitalization among US adults. N. Engl. J. Med. 373, 415\u2013427 (2015).","journal-title":"N. Engl. J. Med."},{"key":"1075_CR9","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.jcv.2014.12.016","volume":"63","author":"S-H Choi","year":"2015","unstructured":"Choi, S.-H. et al. Clinical and molecular characterization of rhinoviruses A, B, and C in adult patients with pneumonia. J. Clin. V. irology 63, 70\u201375 (2015).","journal-title":"J. Clin. V. irology"},{"key":"1075_CR10","doi-asserted-by":"crossref","unstructured":"Palmenberg, A. C. & Gern, J. E. Classification and evolution of human rhinoviruses. Rhinoviruses: methods and protocols, 1\u201310 (2015).","DOI":"10.1007\/978-1-4939-1571-2_1"},{"key":"1075_CR11","doi-asserted-by":"publisher","first-page":"1791","DOI":"10.1099\/vir.0.053686-0","volume":"94","author":"CL McIntyre","year":"2013","unstructured":"McIntyre, C. L., Knowles, N. J. & Simmonds, P. Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types. J. Gen. Virol. 94, 1791\u20131806 (2013).","journal-title":"J. Gen. Virol."},{"key":"1075_CR12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12985-015-0262-z","volume":"12","author":"FE Aponte","year":"2015","unstructured":"Aponte, F. E. et al. Rhinovirus is an important pathogen in upper and lower respiratory tract infections in Mexican children. Virol. J. 12, 1\u20139 (2015).","journal-title":"Virol. J."},{"key":"1075_CR13","doi-asserted-by":"publisher","first-page":"280","DOI":"10.1016\/j.jcv.2011.10.009","volume":"53","author":"C Henquell","year":"2012","unstructured":"Henquell, C. et al. Prospective genotyping of human rhinoviruses in children and adults during the winter of 2009\u20132010. J. Clin. Virol. 53, 280\u2013284 (2012).","journal-title":"J. Clin. Virol."},{"key":"1075_CR14","unstructured":"Howard, L. M. et al. 1 edn ofw001 (Oxford University Press)."},{"key":"1075_CR15","doi-asserted-by":"publisher","first-page":"1876","DOI":"10.1017\/S0950268814002933","volume":"143","author":"J Richter","year":"2015","unstructured":"Richter, J. et al. Molecular epidemiology of rhinoviruses in Cyprus over three consecutive seasons. Epidemiol. Infect. 143, 1876\u20131883 (2015).","journal-title":"Epidemiol. Infect."},{"key":"1075_CR16","doi-asserted-by":"publisher","first-page":"2895","DOI":"10.1128\/JCM.00745-09","volume":"47","author":"Y Jin","year":"2009","unstructured":"Jin, Y. et al. Prevalence and clinical characterization of a newly identified human rhinovirus C species in children with acute respiratory tract infections. J. Clin. Microbiol. 47, 2895\u20132900 (2009).","journal-title":"J. Clin. Microbiol."},{"key":"1075_CR17","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12985-021-01645-6","volume":"18","author":"W Li","year":"2021","unstructured":"Li, W. et al. Genetic diversity and epidemiology of human rhinovirus among children with severe acute respiratory tract infection in Guangzhou, China. Virol. J. 18, 1\u20139 (2021).","journal-title":"Virol. J."},{"key":"1075_CR18","first-page":"1205","volume":"38","author":"C Rundong","year":"2023","unstructured":"Rundong, C. et al. Rhinovirus infection among severe acute respiratory infection cases in hospitalized children in Xuzhou city, Jiangsu province, 2015\u2212 2021. Dis. Surveill. 38, 1205\u20131210 (2023).","journal-title":"Dis. Surveill."},{"key":"1075_CR19","doi-asserted-by":"publisher","first-page":"1983","DOI":"10.1002\/jmv.23861","volume":"86","author":"SZ Zeng","year":"2014","unstructured":"Zeng, S. Z. et al. Prevalence of human rhinovirus in children admitted to hospital with acute lower respiratory tract infections in Changsha, China. J. Med. Virol. 86, 1983\u20131989 (2014).","journal-title":"J. Med. Virol."},{"key":"1075_CR20","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.28531","volume":"95","author":"Q Zhang","year":"2023","unstructured":"Zhang, Q. et al. Identification of two proposed novel human rhinovirus types: Bpat107 and Cpat58. J. Med. Virol. 95, e28531 (2023).","journal-title":"J. Med. Virol."},{"key":"1075_CR21","doi-asserted-by":"publisher","first-page":"1836","DOI":"10.3389\/fmicb.2018.01836","volume":"9","author":"Y Zhao","year":"2018","unstructured":"Zhao, Y. et al. Genotypic diversity and epidemiology of human rhinovirus among children with severe acute respiratory tract infection in Shanghai, 2013\u20132015. Front. Microbiol. 9, 1836 (2018).","journal-title":"Front. Microbiol."},{"key":"1075_CR22","doi-asserted-by":"publisher","first-page":"1111","DOI":"10.1007\/s00705-022-05405-x","volume":"167","author":"H Jiang","year":"2022","unstructured":"Jiang, H. et al. Molecular epidemiology and clinical characterization of human rhinoviruses circulating in Shanghai, 2012-2020. Arch. Virol. 167, 1111\u20131123 (2022).","journal-title":"Arch. Virol."},{"key":"1075_CR23","doi-asserted-by":"publisher","first-page":"2027","DOI":"10.3390\/v13102027","volume":"13","author":"P Golke","year":"2021","unstructured":"Golke, P., H\u00f6nemann, M., Bergs, S. & Liebert, U. G. Human rhinoviruses in adult patients in a tertiary care hospital in Germany: molecular epidemiology and clinical significance. Viruses 13, 2027 (2021).","journal-title":"Viruses"},{"key":"1075_CR24","doi-asserted-by":"publisher","first-page":"1829","DOI":"10.3390\/v14081829","volume":"14","author":"F Neugebauer","year":"2022","unstructured":"Neugebauer, F., Bergs, S., Liebert, U. G. & H\u00f6nemann, M. Human rhinoviruses in pediatric patients in a Tertiary Care Hospital in Germany: molecular epidemiology and clinical significance. Viruses 14, 1829 (2022).","journal-title":"Viruses"},{"key":"1075_CR25","doi-asserted-by":"publisher","first-page":"882","DOI":"10.1136\/thoraxjnl-2019-214317","volume":"75","author":"KT Zlateva","year":"2020","unstructured":"Zlateva, K. T. et al. Molecular epidemiology and clinical impact of rhinovirus infections in adults during three epidemic seasons in 11 European countries (2007\u20132010). Thorax 75, 882\u2013890 (2020).","journal-title":"Thorax"},{"key":"1075_CR26","doi-asserted-by":"publisher","first-page":"341","DOI":"10.3390\/microorganisms12020341","volume":"12","author":"N Berginc","year":"2024","unstructured":"Berginc, N., So\u010dan, M., Prosenc Trilar, K. & Petrovec, M. Seasonality and Genotype Diversity of Human Rhinoviruses during an Eight-Year Period in Slovenia. Microorganisms 12, 341 (2024).","journal-title":"Microorganisms"},{"key":"1075_CR27","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-78628-4","volume":"14","author":"DM Sardinha","year":"2024","unstructured":"Sardinha, D. M., Silva, M. J. A., Lima, K. V. B. & Lima, L. N. G. C. Factors associated with outcome in a national cohort of rhinovirus hospitalized patients in Brazil in 2022. Sci. Rep. 14, 27413 (2024).","journal-title":"Sci. Rep."},{"key":"1075_CR28","doi-asserted-by":"publisher","first-page":"e2193","DOI":"10.1002\/rmv.2193","volume":"31","author":"H Ortega","year":"2021","unstructured":"Ortega, H., Nickle, D. & Carter, L. Rhinovirus and asthma: Challenges and opportunities. Rev. Med. Virol. 31, e2193 (2021).","journal-title":"Rev. Med. Virol."},{"key":"1075_CR29","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1016\/j.jaip.2022.01.006","volume":"10","author":"DJ Jackson","year":"2022","unstructured":"Jackson, D. J. & Gern, J. E. Rhinovirus infections and their roles in asthma: etiology and exacerbations. J. Allergy Clin. Immunology: Pract. 10, 673\u2013681 (2022).","journal-title":"J. Allergy Clin. Immunology: Pract."},{"key":"1075_CR30","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1016\/j.resinv.2021.08.009","volume":"60","author":"K Kan-o","year":"2022","unstructured":"Kan-o, K. et al. Differences in the spectrum of respiratory viruses and detection of human rhinovirus C in exacerbations of adult asthma and chronic obstructive pulmonary disease. Respiratory Investig. 60, 129\u2013136 (2022).","journal-title":"Respiratory Investig."},{"key":"1075_CR31","doi-asserted-by":"publisher","first-page":"1620","DOI":"10.3390\/microorganisms8101620","volume":"8","author":"C Biagi","year":"2020","unstructured":"Biagi, C., Rocca, A., Poletti, G., Fabi, M. & Lanari, M. Rhinovirus infection in children with acute bronchiolitis and its impact on recurrent wheezing and asthma development. Microorganisms 8, 1620 (2020).","journal-title":"Microorganisms"},{"key":"1075_CR32","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1128\/CMR.00032-09","volume":"23","author":"S Tregoning John","year":"2010","unstructured":"Tregoning John, S. & Schwarze, J. Respiratory Viral Infections in Infants: Causes, Clinical Symptoms, Virology, and Immunology. Clin. Microbiol. Rev. 23, 74\u201398 (2010).","journal-title":"Clin. Microbiol. Rev."},{"key":"1075_CR33","doi-asserted-by":"publisher","first-page":"704","DOI":"10.1016\/j.chom.2015.03.008","volume":"17","author":"ShuM Teo","year":"2015","unstructured":"Teo, S. huM. et al. The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development. Cell Host Microbe 17, 704\u2013715 (2015).","journal-title":"Cell Host Microbe"},{"key":"1075_CR34","unstructured":"de Steenhuijsen Piters, W. A. et al. Nasopharyngeal Microbiota, Host Transcriptome, and Disease Severity in Children with Respiratory Syncytial Virus Infection."},{"key":"1075_CR35","unstructured":"Rosas-Salazar, C. et al. Nasopharyngeal Microbiome in Respiratory Syncytial Virus Resembles Profile Associated with Increased Childhood Asthma Risk."},{"key":"1075_CR36","unstructured":"Dissanayake, E. et al. Rhinovirus increases Moraxella catarrhalis adhesion to the respiratory epithelium."},{"key":"1075_CR37","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-015-1081-y","volume":"15","author":"JJ Hofstra","year":"2015","unstructured":"Hofstra, J. J. et al. Changes in microbiota during experimental human Rhinovirus infection. BMC Infect. Dis. 15, 336 (2015).","journal-title":"BMC Infect. Dis."},{"key":"1075_CR38","unstructured":"F\u00f8lsgaard, N. V. et al. Pathogenic bacteria colonizing the airways in asymptomatic neonates stimulates topical inflammatory mediator release."},{"key":"1075_CR39","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1038\/s41579-022-00807-9","volume":"21","author":"EJ Chow","year":"2023","unstructured":"Chow, E. J., Uyeki, T. M. & Chu, H. Y. The effects of the COVID-19 pandemic on community respiratory virus activity. Nat. Rev. Microbiol. 21, 195\u2013210 (2023).","journal-title":"Nat. Rev. Microbiol."},{"key":"1075_CR40","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-82660-9","volume":"14","author":"X Xu","year":"2024","unstructured":"Xu, X., Zhang, Y., Xu, L., Jiang, W. & Hao, C. Analysis of respiratory pathogen detection in hospitalized children with acute respiratory tract infections after ending the zero COVID policy. Sci. Rep. 14, 31784 (2024).","journal-title":"Sci. Rep."},{"key":"1075_CR41","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1002\/jmv.20588","volume":"78","author":"B Winther","year":"2006","unstructured":"Winther, B., Hayden, F. G. & Hendley, J. O. Picornavirus infections in children diagnosed by RT-PCR during longitudinal surveillance with weekly sampling: association with symptomatic illness and effect of season. J. Med. Virol. 78, 644\u2013650 (2006).","journal-title":"J. Med. Virol."},{"key":"1075_CR42","doi-asserted-by":"publisher","first-page":"1261","DOI":"10.1056\/NEJM196612082752301","volume":"275","author":"JM Gwaltney Jr","year":"1966","unstructured":"Gwaltney, J. M. Jr, Hendley, J. O., Simon, G. & Jordan, W. S. Jr Rhinovirus infections in an industrial population: the occurrence of illness. N. Engl. J. Med. 275, 1261\u20131268 (1966).","journal-title":"N. Engl. J. Med."},{"key":"1075_CR43","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1016\/j.jcv.2014.10.006","volume":"61","author":"DN Marcone","year":"2014","unstructured":"Marcone, D. N., Culasso, A., Carballal, G., Campos, R. & Echavarr\u00eda, M. Genetic diversity and clinical impact of human rhinoviruses in hospitalized and outpatient children with acute respiratory infection, Argentina. J. Clin. Virol. 61, 558\u2013564 (2014).","journal-title":"J. Clin. Virol."},{"key":"1075_CR44","doi-asserted-by":"publisher","first-page":"1665","DOI":"10.3201\/eid1410.080545","volume":"14","author":"Z Xiang","year":"2008","unstructured":"Xiang, Z. et al. Human rhinovirus group C infection in children with lower respiratory tract infection. Emerg. Infect. Dis. 14, 1665 (2008).","journal-title":"Emerg. Infect. Dis."},{"key":"1075_CR45","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/2049-2618-2-22","volume":"2","author":"EK Allen","year":"2014","unstructured":"Allen, E. K. et al. Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge. Microbiome 2, 1\u201311 (2014).","journal-title":"Microbiome"},{"key":"1075_CR46","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-02322-y","volume":"11","author":"AE Tozzi","year":"2021","unstructured":"Tozzi, A. E. et al. Nasopharyngeal microbiota in hospitalized children with Bordetella pertussis and Rhinovirus infection. Sci. Rep. 11, 22858 (2021).","journal-title":"Sci. Rep."},{"key":"1075_CR47","doi-asserted-by":"publisher","first-page":"1224","DOI":"10.1164\/rccm.201302-0341OC","volume":"188","author":"PL Molyneaux","year":"2013","unstructured":"Molyneaux, P. L. et al. Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of chronic obstructive pulmonary disease. Am. J. Respiratory Crit. Care Med. 188, 1224\u20131231 (2013).","journal-title":"Am. J. Respiratory Crit. Care Med."},{"key":"1075_CR48","doi-asserted-by":"publisher","first-page":"14691","DOI":"10.1073\/pnas.1005963107","volume":"107","author":"C De Filippo","year":"2010","unstructured":"De Filippo, C. et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. USA 107, 14691\u201314696 (2010).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"1075_CR49","doi-asserted-by":"publisher","first-page":"560","DOI":"10.1126\/science.aad3503","volume":"352","author":"G Falony","year":"2016","unstructured":"Falony, G. et al. Population-level analysis of gut microbiome variation. Science 352, 560\u2013564 (2016).","journal-title":"Science"},{"key":"1075_CR50","doi-asserted-by":"publisher","first-page":"1532","DOI":"10.1038\/s41591-018-0164-x","volume":"24","author":"Y He","year":"2018","unstructured":"He, Y. et al. Regional variation limits applications of healthy gut microbiome reference ranges and disease models. Nat. Med. 24, 1532\u20131535 (2018).","journal-title":"Nat. Med."},{"key":"1075_CR51","doi-asserted-by":"publisher","first-page":"6","DOI":"10.3390\/microorganisms5010006","volume":"5","author":"DJ Lisko","year":"2017","unstructured":"Lisko, D. J., Johnston, G. P. & Johnston, C. G. Effects of dietary yogurt on the healthy human gastrointestinal (GI) microbiome. Microorganisms 5, 6 (2017).","journal-title":"Microorganisms"},{"key":"1075_CR52","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/nature11053","volume":"486","author":"T Yatsunenko","year":"2012","unstructured":"Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. nature 486, 222\u2013227 (2012).","journal-title":"nature"},{"key":"1075_CR53","doi-asserted-by":"publisher","first-page":"859","DOI":"10.3390\/nu9080859","volume":"9","author":"K Lau","year":"2017","unstructured":"Lau, K. et al. Bridging the gap between gut microbial dysbiosis and cardiovascular diseases. Nutrients 9, 859 (2017).","journal-title":"Nutrients"},{"key":"1075_CR54","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-49195-w","volume":"9","author":"S Gomes","year":"2019","unstructured":"Gomes, S. et al. Profiling of lung microbiota discloses differences in adenocarcinoma and squamous cell carcinoma. Sci. Rep. 9, 12838 (2019).","journal-title":"Sci. Rep."},{"key":"1075_CR55","doi-asserted-by":"publisher","first-page":"1101","DOI":"10.1007\/s10096-013-2044-0","volume":"33","author":"L Millares","year":"2014","unstructured":"Millares, L. et al. Bronchial microbiome of severe COPD patients colonised by Pseudomonas aeruginosa. Eur. J. Clin. Microbiol. Infect. Dis. 33, 1101\u20131111 (2014).","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"1075_CR56","doi-asserted-by":"publisher","first-page":"e17035","DOI":"10.1371\/journal.pone.0017035","volume":"6","author":"D Bogaert","year":"2011","unstructured":"Bogaert, D. et al. Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis. PloS one 6, e17035 (2011).","journal-title":"PloS one"},{"key":"1075_CR57","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1177\/194589240301700406","volume":"17","author":"DH Chi","year":"2003","unstructured":"Chi, D. H. et al. Nasopharyngeal reservoir of bacterial otitis media and sinusitis pathogens in adults during wellness and viral respiratory illness. Am. J. Rhinol. 17, 209\u2013214 (2003).","journal-title":"Am. J. Rhinol."},{"key":"1075_CR58","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1093\/jac\/dkf506","volume":"50","author":"J\u00c1 Garc\u00eda-Rodr\u00edguez","year":"2002","unstructured":"Garc\u00eda-Rodr\u00edguez, J. \u00c1 & Fresnadillo Mart\u00ednez, M. J. Dynamics of nasopharyngeal colonization by potential respiratory pathogens. J. Antimicrobial Chemother. 50, 59\u201374 (2002).","journal-title":"J. Antimicrobial Chemother."},{"key":"1075_CR59","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1016\/j.prrv.2012.04.001","volume":"13","author":"SI Pelton","year":"2012","unstructured":"Pelton, S. I. Regulation of bacterial trafficking in the nasopharynx. Paediatr. respiratory Rev. 13, 150\u2013153 (2012).","journal-title":"Paediatr. respiratory Rev."},{"key":"1075_CR60","doi-asserted-by":"publisher","first-page":"e3846","DOI":"10.1371\/journal.pone.0003846","volume":"3","author":"D Sevillano","year":"2008","unstructured":"Sevillano, D. et al. \u03b2-Lactam effects on mixed cultures of common respiratory isolates as an approach to treatment effects on nasopharyngeal bacterial population dynamics. PLoS One 3, e3846 (2008).","journal-title":"PLoS One"},{"key":"1075_CR61","doi-asserted-by":"publisher","first-page":"1301","DOI":"10.1016\/j.jaci.2014.02.030","volume":"133","author":"KM Kloepfer","year":"2014","unstructured":"Kloepfer, K. M. et al. Detection of pathogenic bacteria during rhinovirus infection is associated with increased respiratory symptoms and asthma exacerbations. J. allergy Clin. Immunol. 133, 1301\u20131307 (2014).","journal-title":"J. allergy Clin. Immunol."},{"key":"1075_CR62","doi-asserted-by":"publisher","first-page":"1909","DOI":"10.1016\/j.jaci.2016.01.036","volume":"137","author":"JM Mansbach","year":"2016","unstructured":"Mansbach, J. M. et al. Respiratory syncytial virus and rhinovirus severe bronchiolitis are associated with distinct nasopharyngeal microbiota. J. Allergy Clin. Immunol. 137, 1909\u20131913 (2016).","journal-title":"J. Allergy Clin. Immunol."},{"key":"1075_CR63","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1111\/1462-2920.14009","volume":"20","author":"J Feng","year":"2018","unstructured":"Feng, J. et al. Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses. Environ. Microbiol. 20, 355\u2013368 (2018).","journal-title":"Environ. Microbiol."},{"key":"1075_CR64","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2020.590018","volume":"7","author":"Q Qiu","year":"2020","unstructured":"Qiu, Q. et al. Metagenomic analysis reveals the distribution of antibiotic resistance genes in a large-scale population of healthy individuals and patients with varied diseases. Front. Mol. Biosci. 7, 590018 (2020).","journal-title":"Front. Mol. Biosci."},{"key":"1075_CR65","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1038\/nature13377","volume":"509","author":"KJ Forsberg","year":"2014","unstructured":"Forsberg, K. J. et al. Bacterial phylogeny structures soil resistomes across habitats. Nature 509, 612\u2013616 (2014).","journal-title":"Nature"},{"key":"1075_CR66","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aap8914","volume":"10","author":"A Vich Vila","year":"2018","unstructured":"Vich Vila, A. et al. Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Sci. Transl. Med. 10, eaap8914 (2018).","journal-title":"Sci. Transl. Med."},{"key":"1075_CR67","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/j.mib.2020.02.002","volume":"53","author":"RS McInnes","year":"2020","unstructured":"McInnes, R. S., McCallum, G. E., Lamberte, L. E. & van Schaik, W. Horizontal transfer of antibiotic resistance genes in the human gut microbiome. Curr. Opin. Microbiol. 53, 35\u201343 (2020).","journal-title":"Curr. Opin. Microbiol."},{"key":"1075_CR68","doi-asserted-by":"publisher","first-page":"2490","DOI":"10.1038\/ismej.2015.59","volume":"9","author":"B Li","year":"2015","unstructured":"Li, B. et al. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. ISME J. 9, 2490\u20132502 (2015).","journal-title":"ISME J."},{"key":"1075_CR69","doi-asserted-by":"publisher","DOI":"10.1016\/j.virusres.2021.198408","volume":"300","author":"S Abbasi","year":"2021","unstructured":"Abbasi, S. et al. Impact of human rhinoviruses on gene expression in pediatric patients with severe acute respiratory infection. Virus Res. 300, 198408 (2021).","journal-title":"Virus Res."},{"key":"1075_CR70","doi-asserted-by":"publisher","first-page":"e1005111","DOI":"10.1371\/journal.pgen.1005111","volume":"11","author":"M \u00c7al\u0131\u015fkan","year":"2015","unstructured":"\u00c7al\u0131\u015fkan, M., Baker, S. W., Gilad, Y. & Ober, C. Host genetic variation influences gene expression response to rhinovirus infection. PLoS Genet. 11, e1005111 (2015).","journal-title":"PLoS Genet."},{"key":"1075_CR71","doi-asserted-by":"publisher","first-page":"1327","DOI":"10.3389\/fimmu.2020.01327","volume":"11","author":"K-M Ling","year":"2020","unstructured":"Ling, K.-M. et al. Rhinovirus infection drives complex host airway molecular responses in children with cystic fibrosis. Front. Immunol. 11, 1327 (2020).","journal-title":"Front. Immunol."},{"key":"1075_CR72","unstructured":"GeneCards. The Human Gene Database. (2024)."},{"key":"1075_CR73","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1016\/j.virol.2015.08.014","volume":"486","author":"T-K Kim","year":"2015","unstructured":"Kim, T.-K. et al. A systems approach to understanding human rhinovirus and influenza virus infection. Virology 486, 146\u2013157 (2015).","journal-title":"Virology"},{"key":"1075_CR74","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1016\/j.jaci.2008.08.013","volume":"122","author":"JT Kelly","year":"2008","unstructured":"Kelly, J. T. & Busse, W. W. Host immune responses to rhinovirus: mechanisms in asthma. J. Allergy Clin. Immunol. 122, 671\u2013682 (2008).","journal-title":"J. Allergy Clin. Immunol."},{"key":"1075_CR75","doi-asserted-by":"crossref","unstructured":"Glickman, M. H. & Ciechanover, A. The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Physiological reviews (2002).","DOI":"10.1152\/physrev.00027.2001"},{"key":"1075_CR76","doi-asserted-by":"publisher","first-page":"e0213501","DOI":"10.1371\/journal.pone.0213501","volume":"14","author":"SE Vieira","year":"2019","unstructured":"Vieira, S. E. et al. Distinct transcriptional modules in the peripheral blood mononuclear cells response to human respiratory syncytial virus or to human rhinovirus in hospitalized infants with bronchiolitis. PLoS ONE 14, e0213501 (2019).","journal-title":"PLoS ONE"},{"key":"1075_CR77","doi-asserted-by":"publisher","first-page":"730","DOI":"10.1038\/ni1087","volume":"5","author":"M Yoneyama","year":"2004","unstructured":"Yoneyama, M. et al. The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses. Nat. Immunol. 5, 730\u2013737 (2004).","journal-title":"Nat. Immunol."},{"key":"1075_CR78","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1038\/s41421-021-00248-3","volume":"7","author":"B Lu","year":"2021","unstructured":"Lu, B. et al. Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs. Cell Discov. 7, 19 (2021).","journal-title":"Cell Discov."},{"key":"1075_CR79","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884\u2013i890 (2018).","journal-title":"Bioinformatics"},{"key":"1075_CR80","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. methods 9, 357\u2013359 (2012).","journal-title":"Nat. methods"},{"key":"1075_CR81","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"key":"1075_CR82","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-019-1891-0","volume":"20","author":"DE Wood","year":"2019","unstructured":"Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20, 1\u201313 (2019).","journal-title":"Genome Biol."},{"key":"1075_CR83","doi-asserted-by":"publisher","DOI":"10.7717\/peerj-cs.104","volume":"3","author":"J Lu","year":"2017","unstructured":"Lu, J., Breitwieser, F. P., Thielen, P. & Salzberg, S. L. Bracken: estimating species abundance in metagenomics data. PeerJ Computer Sci. 3, e104 (2017).","journal-title":"PeerJ Computer Sci."},{"key":"1075_CR84","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","volume":"30","author":"Y Liao","year":"2014","unstructured":"Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923\u2013930 (2014).","journal-title":"Bioinformatics"},{"key":"1075_CR85","doi-asserted-by":"publisher","first-page":"lqaa078","DOI":"10.1093\/nargab\/lqaa078","volume":"2","author":"Y Zhang","year":"2020","unstructured":"Zhang, Y., Parmigiani, G. & Johnson, W. E. ComBat-seq: batch effect adjustment for RNA-seq count data. NAR genomics Bioinforma. 2, lqaa078 (2020).","journal-title":"NAR genomics Bioinforma."},{"key":"1075_CR86","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 1\u201321 (2014).","journal-title":"Genome Biol."},{"key":"1075_CR87","doi-asserted-by":"crossref","unstructured":"Wu, T. et al. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation 2 (2021).","DOI":"10.1016\/j.xinn.2021.100141"},{"key":"1075_CR88","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkac920","volume":"51","author":"BP Alcock","year":"2023","unstructured":"Alcock, B. P. et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic acids Res. 51, D690\u2013D699 (2023).","journal-title":"Nucleic acids Res."},{"key":"1075_CR89","doi-asserted-by":"publisher","first-page":"3896","DOI":"10.1111\/1462-2920.13370","volume":"18","author":"HW Hu","year":"2016","unstructured":"Hu, H. W. et al. Field-based evidence for copper contamination induced changes of antibiotic resistance in agricultural soils. Environ. Microbiol. 18, 3896\u20133909 (2016).","journal-title":"Environ. Microbiol."}],"container-title":["npj Biofilms and Microbiomes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41522-026-01075-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41522-026-01075-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41522-026-01075-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T00:03:34Z","timestamp":1792713814000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41522-026-01075-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,2]]},"references-count":89,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["1075"],"URL":"https:\/\/doi.org\/10.1038\/s41522-026-01075-8","relation":{},"ISSN":["2055-5008"],"issn-type":[{"value":"2055-5008","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,2]]},"assertion":[{"value":"9 October 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 June 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 July 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}],"article-number":"210"}}