Altered airway microbiota and microbial biomarkers across respiratory diseases: insights from 16S rDNA sequencing

Altered airway microbiota and microbial biomarkers across respiratory diseases: insights from 16S rDNA sequencing | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Altered airway microbiota and microbial biomarkers across respiratory diseases: insights from 16S rDNA sequencing Huifang Song, Maoye Xu, Jia Wang, Lemei Mo, Chunmeng Shan, Xuejie Bai, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8035911/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Objective The airway microbiota plays an important role in respiratory health and disease, yet comprehensive comparisons of microbial alterations across different respiratory disorders remain limited. Methods We performed 16S rDNA sequencing to characterize the airway microbiota in patients with chronic obstructive pulmonary disease (COPD, n = 53), bronchial asthma (BA, n = 38), pneumonia (PNE, n = 25), chronic cough (CC, n = 21), bronchitis (BRO, n = 4), and lung cancer (CA, n = 3), alongside healthy controls (NC, n = 9). Microbial richness, alpha and beta diversity, taxonomic composition, and disease-specific microbial biomarkers were systematically analyzed. Results Microbial richness and diversity were significantly reduced in respiratory diseases compared with controls, particularly in CA and BRO. Beta diversity analysis revealed distinct clustering, with COPD, BA, and PNE forming Firmicutes-dominated clusters, while CA and BRO clustered separately with Proteobacteria dominance. CC and NC shared similar profiles. MetaStat analysis showed enrichment of Firmicutes in COPD and PNE, Proteobacteria in CA, and unclassified taxa in CC. Linear discriminant analysis identified biomarkers like Rothia in COPD, Veillonella in PNE, Haemophilus in BA, Neisseria in CA, and Neisseria subflava in BRO, with healthy controls enriched in Clostridia. Conclusion Our findings reveal that airway microbial communities are profoundly altered in respiratory diseases, characterized by reduced diversity, disease-specific clustering, and distinct microbial biomarkers. These results highlight the potential of airway microbiota as diagnostic indicators and provide insights into the pathophysiological roles of microbial dysbiosis in respiratory diseases. Airway microbiota respiratory diseases 16S rDNA sequencing microbial diversity microbial biomarkers Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8035911","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":561116854,"identity":"d3256131-136b-4f6d-8be6-dcfcf25b3c2c","order_by":0,"name":"Huifang Song","email":"","orcid":"","institution":"Inner Mongolia People’s Hospital","correspondingAuthor":false,"prefix":"","firstName":"Huifang","middleName":"","lastName":"Song","suffix":""},{"id":561116857,"identity":"7bfd53f3-4e3b-45fb-95e0-0545edf54c53","order_by":1,"name":"Maoye Xu","email":"","orcid":"","institution":"Inner Mongolia People’s 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sequencing","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Airway microbiota, respiratory diseases, 16S rDNA sequencing, microbial diversity, microbial biomarkers","lastPublishedDoi":"10.21203/rs.3.rs-8035911/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8035911/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eObjective\u003c/h2\u003e \u003cp\u003eThe airway microbiota plays an important role in respiratory health and disease, yet comprehensive comparisons of microbial alterations across different respiratory disorders remain limited.\u003c/p\u003e\u003ch2\u003eMethods\u003c/h2\u003e \u003cp\u003eWe performed 16S rDNA sequencing to characterize the airway microbiota in patients with chronic obstructive pulmonary disease (COPD, n\u0026thinsp;=\u0026thinsp;53), bronchial asthma (BA, n\u0026thinsp;=\u0026thinsp;38), pneumonia (PNE, n\u0026thinsp;=\u0026thinsp;25), chronic cough (CC, n\u0026thinsp;=\u0026thinsp;21), bronchitis (BRO, n\u0026thinsp;=\u0026thinsp;4), and lung cancer (CA, n\u0026thinsp;=\u0026thinsp;3), alongside healthy controls (NC, n\u0026thinsp;=\u0026thinsp;9). Microbial richness, alpha and beta diversity, taxonomic composition, and disease-specific microbial biomarkers were systematically analyzed.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eMicrobial richness and diversity were significantly reduced in respiratory diseases compared with controls, particularly in CA and BRO. Beta diversity analysis revealed distinct clustering, with COPD, BA, and PNE forming Firmicutes-dominated clusters, while CA and BRO clustered separately with Proteobacteria dominance. CC and NC shared similar profiles. MetaStat analysis showed enrichment of Firmicutes in COPD and PNE, Proteobacteria in CA, and unclassified taxa in CC. Linear discriminant analysis identified biomarkers like Rothia in COPD, Veillonella in PNE, Haemophilus in BA, Neisseria in CA, and Neisseria subflava in BRO, with healthy controls enriched in Clostridia.\u003c/p\u003e\u003ch2\u003eConclusion\u003c/h2\u003e \u003cp\u003eOur findings reveal that airway microbial communities are profoundly altered in respiratory diseases, characterized by reduced diversity, disease-specific clustering, and distinct microbial biomarkers. These results highlight the potential of airway microbiota as diagnostic indicators and provide insights into the pathophysiological roles of microbial dysbiosis in respiratory diseases.\u003c/p\u003e","manuscriptTitle":"Altered airway microbiota and microbial biomarkers across respiratory diseases: insights from 16S rDNA sequencing","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-12-18 13:20:29","doi":"10.21203/rs.3.rs-8035911/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"2a1c8f4e-1417-48ef-9e75-dddee7b288be","owner":[],"postedDate":"December 18th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2026-02-23T05:55:41+00:00","versionOfRecord":[],"versionCreatedAt":"2025-12-18 13:20:29","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8035911","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8035911","identity":"rs-8035911","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}