Enrichment of oral-associated microbiota in bronchoalveolar lavage fluid is associated with altered immune markers in aspiration pneumonia, with Gemella linked to in-hospital mortality

Enrichment of oral-associated microbiota in bronchoalveolar lavage fluid is associated with altered immune markers in aspiration pneumonia, with Gemella linked to in-hospital mortality | 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 Enrichment of oral-associated microbiota in bronchoalveolar lavage fluid is associated with altered immune markers in aspiration pneumonia, with Gemella linked to in-hospital mortality Runze Wang, Yiru Shao, Lin Zhang, Chen Zhang, Weichun Mo, Feng Zhang, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8863633/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 5 You are reading this latest preprint version Abstract Background Aspiration pneumonia (AP) is common and life-threatening among hospitalized patients, particularly older adults. However, the lower respiratory tract microbiome in AP and its clinical relevance remain incompletely understood. Methods We conducted a single-center retrospective study of intensive care unit patients and profiled bronchoalveolar lavage fluid (BALF) microbiota using metagenomic next-generation sequencing (mNGS). BALF samples were obtained from 49 patients with AP and 23 patients with community-acquired pneumonia (CAP). Alpha diversity (Shannon/Simpson) and beta diversity (Bray–Curtis; PERMANOVA) were compared between groups. Differentially abundant taxa were identified and correlated with inflammatory and immune markers using Spearman correlation with false discovery rate (FDR) correction. Within AP, associations between Gemella detection and in-hospital mortality were assessed using logistic regression adjusted for age, APACHE II score, and CD3 + percentage. Results Alpha diversity was significantly higher in AP than in CAP (Shannon p = 0.008; Simpson p = 0.0068). In contrast, the overall community structure showed no significant difference between the groups (PERMANOVA R² = 0.022, p = 0.066). AP samples were enriched in oral-associated genera including Streptococcus and Rothia and depleted in Acinetobacter and Stenotrophomonas . Streptococcus abundance correlated positively with lactate, procalcitonin, and NK cell percentage, and negatively with CD3 + and CD8 + T-cell proportions. Within AP, overall microbiome profiles were broadly similar between survivors and non-survivors; however, non-survivors had higher Gemella abundance and a higher detection rate (30.8% vs 4.3%, Fisher’s exact p = 0.026). Gemella detection was associated with in-hospital mortality in univariate analysis and showed a non-significant trend after multivariable adjustment (adjusted OR 6.81, 95% CI 0.67–69.58; p = 0.106). Conclusions AP was characterized by enrichment of oral-associated taxa in BALF that were associated with inflammatory and cellular immune alterations. Gemella abundance and detection may be linked to in-hospital mortality in AP, warranting validation in larger prospective cohorts. aspiration pneumonia bronchoalveolar lavage fluid metagenomic next-generation sequencing immune markers prognosis Full Text Additional Declarations No competing interests reported. Supplementary Files Supplementarymaterial.tar Cite Share Download PDF Status: Under Review Version 1 posted Reviewers invited by journal 17 Mar, 2026 Editor assigned by journal 16 Mar, 2026 Editor invited by journal 23 Feb, 2026 Submission checks completed at journal 21 Feb, 2026 First submitted to journal 21 Feb, 2026 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-8863633","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":607693893,"identity":"48bf18c8-9a71-4007-b03c-d1ae7c64f9e0","order_by":0,"name":"Runze Wang","email":"","orcid":"","institution":"Jinshan Hospital of Fudan University","correspondingAuthor":false,"prefix":"","firstName":"Runze","middleName":"","lastName":"Wang","suffix":""},{"id":607693894,"identity":"2efd8956-31a9-42f9-a1d8-5fd732f3bafb","order_by":1,"name":"Yiru Shao","email":"","orcid":"","institution":"Jinshan Hospital of Fudan 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mortality","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"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":"bmc-pulmonary-medicine","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pulm","sideBox":"Learn more about [BMC Pulmonary Medicine](http://bmcpulmmed.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/pulm/default.aspx","title":"BMC Pulmonary Medicine","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"aspiration pneumonia, bronchoalveolar lavage fluid, metagenomic next-generation sequencing, immune markers, prognosis","lastPublishedDoi":"10.21203/rs.3.rs-8863633/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8863633/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003eAspiration pneumonia (AP) is common and life-threatening among hospitalized patients, particularly older adults. However, the lower respiratory tract microbiome in AP and its clinical relevance remain incompletely understood.\u003c/p\u003e\u003ch2\u003eMethods\u003c/h2\u003e \u003cp\u003eWe conducted a single-center retrospective study of intensive care unit patients and profiled bronchoalveolar lavage fluid (BALF) microbiota using metagenomic next-generation sequencing (mNGS). BALF samples were obtained from 49 patients with AP and 23 patients with community-acquired pneumonia (CAP). Alpha diversity (Shannon/Simpson) and beta diversity (Bray\u0026ndash;Curtis; PERMANOVA) were compared between groups. Differentially abundant taxa were identified and correlated with inflammatory and immune markers using Spearman correlation with false discovery rate (FDR) correction. Within AP, associations between \u003cem\u003eGemella\u003c/em\u003e detection and in-hospital mortality were assessed using logistic regression adjusted for age, APACHE II score, and CD3\u003csup\u003e+\u003c/sup\u003e percentage.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eAlpha diversity was significantly higher in AP than in CAP (Shannon p\u0026thinsp;=\u0026thinsp;0.008; Simpson p\u0026thinsp;=\u0026thinsp;0.0068). In contrast, the overall community structure showed no significant difference between the groups (PERMANOVA R\u0026sup2; = 0.022, p\u0026thinsp;=\u0026thinsp;0.066). AP samples were enriched in oral-associated genera including \u003cem\u003eStreptococcus\u003c/em\u003e and \u003cem\u003eRothia\u003c/em\u003e and depleted in \u003cem\u003eAcinetobacter\u003c/em\u003e and \u003cem\u003eStenotrophomonas\u003c/em\u003e. \u003cem\u003eStreptococcus\u003c/em\u003e abundance correlated positively with lactate, procalcitonin, and NK cell percentage, and negatively with CD3\u003csup\u003e+\u003c/sup\u003e and CD8\u003csup\u003e+\u003c/sup\u003e T-cell proportions. Within AP, overall microbiome profiles were broadly similar between survivors and non-survivors; however, non-survivors had higher \u003cem\u003eGemella\u003c/em\u003e abundance and a higher detection rate (30.8% vs 4.3%, Fisher\u0026rsquo;s exact p\u0026thinsp;=\u0026thinsp;0.026). \u003cem\u003eGemella\u003c/em\u003e detection was associated with in-hospital mortality in univariate analysis and showed a non-significant trend after multivariable adjustment (adjusted OR 6.81, 95% CI 0.67\u0026ndash;69.58; p\u0026thinsp;=\u0026thinsp;0.106).\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e \u003cp\u003eAP was characterized by enrichment of oral-associated taxa in BALF that were associated with inflammatory and cellular immune alterations. Gemella abundance and detection may be linked to in-hospital mortality in AP, warranting validation in larger prospective cohorts.\u003c/p\u003e","manuscriptTitle":"Enrichment of oral-associated microbiota in bronchoalveolar lavage fluid is associated with altered immune markers in aspiration pneumonia, with Gemella linked to in-hospital mortality","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-18 22:20:27","doi":"10.21203/rs.3.rs-8863633/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"reviewersInvited","content":"","date":"2026-03-17T06:45:18+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-03-16T13:10:33+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2026-02-23T09:34:03+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-02-21T16:05:48+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Pulmonary Medicine","date":"2026-02-21T16:00:17+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-pulmonary-medicine","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pulm","sideBox":"Learn more about [BMC Pulmonary Medicine](http://bmcpulmmed.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/pulm/default.aspx","title":"BMC Pulmonary Medicine","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"ea0da8be-5066-4e34-bd54-6c7078dcbe69","owner":[],"postedDate":"March 18th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-03-18T22:20:27+00:00","versionOfRecord":[],"versionCreatedAt":"2026-03-18 22:20:27","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8863633","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8863633","identity":"rs-8863633","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}