Integration of Donor Microbiota Following FMT Predicts Anti–PD-1 Response in Melanoma

Integration of Donor Microbiota Following FMT Predicts Anti–PD-1 Response in Melanoma | 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 Analysis Integration of Donor Microbiota Following FMT Predicts Anti–PD-1 Response in Melanoma Justin Sonnenburg, Jessica Fessler, Matthew Olm, Edgar Engleman This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7483676/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Fecal microbiota transplantation (FMT) has shown promise improving anti–PD-1 therapy in melanoma, but the underlying microbial features remain poorly defined. We performed strain-resolved metagenomic analysis of three clinical trials and found therapeutic benefit was linked to successful integration of donor microbiota, rather than increased diversity or engraftment of specific species. Responders acquired more donor-derived strains, exhibited greater post-FMT similarity to their donor, and maintained a more stable microbial community. Non-responders showed greater shifts in taxonomic composition and estimated microbial load relative to baseline, and increased abundance of pathogen-associated secretion system genes. In responders, microbial functions involved in community-level metabolism and communication, including the phosphotransferase system and quorum sensing, were more prominent. Finally, tumor-infiltrating immune profiles tracked with clinical outcomes and microbiome changes. Together these findings highlight that distinct patterns of microbiome restructuring, including stable community transitions and enriched functional capacity, are associated with anti–PD-1 response following FMT. Biological sciences/Microbiology/Microbial communities/Microbiome Biological sciences/Computational biology and bioinformatics/Data integration Biological sciences/Cancer/Skin cancer/Melanoma Biological sciences/Immunology/Immunotherapy Biological sciences/Cancer/Tumour immunology Full Text Additional Declarations There is NO Competing Interest. Cite Share Download PDF Status: Under Review 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. 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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-7483676","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Analysis","associatedPublications":[],"authors":[{"id":510318350,"identity":"e5e95735-37fd-4490-95d6-f53db3ac0a46","order_by":0,"name":"Justin Sonnenburg","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABA0lEQVRIiWNgGAWjYBACxgYInQBiPwCx2IEiEgwMzERpYTYAUTwHCGiBAZAWNgmitDD3Hz72uKDiTp7B7ePXKn/+sMvjYe99eIOhwjqxAZfDZqSlG88486zY4FxO2W2ehORiHp7jxhYMZ9LxaOExk+ZtO5y44QxP2m2GBObE/RJpbBKMQBGcWvrPALX8g2gp/JFQn9gD1vIPj5aGHKCWBpAW9mMMPAmHoVoa8GiZkZYmzXPscLHkGR5maZ6044k9PMeYLRKOpRvj0mIIDDFpnprDeXxn2B9+/GFTndjD3sZ440ONtSxOLQgJHgOEcAIO5SAgj2CyP8CjbhSMglEwCkYyAABq41qXXZmN6AAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0003-2299-6817","institution":"Stanford University","correspondingAuthor":true,"prefix":"","firstName":"Justin","middleName":"","lastName":"Sonnenburg","suffix":""},{"id":510318351,"identity":"62cf30a5-aca9-424e-97fa-cc74060506a7","order_by":1,"name":"Jessica Fessler","email":"","orcid":"","institution":"Stanford University","correspondingAuthor":false,"prefix":"","firstName":"Jessica","middleName":"","lastName":"Fessler","suffix":""},{"id":510318352,"identity":"a8f412bc-0965-4eff-a999-0549256717c8","order_by":2,"name":"Matthew Olm","email":"","orcid":"","institution":"University of Colorado Boulder","correspondingAuthor":false,"prefix":"","firstName":"Matthew","middleName":"","lastName":"Olm","suffix":""},{"id":510318353,"identity":"d1f78909-257f-4714-9161-644d665a462e","order_by":3,"name":"Edgar Engleman","email":"","orcid":"https://orcid.org/0000-0002-2096-9279","institution":"Stanford University","correspondingAuthor":false,"prefix":"","firstName":"Edgar","middleName":"","lastName":"Engleman","suffix":""}],"badges":[],"createdAt":"2025-08-28 23:55:18","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7483676/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7483676/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":93266689,"identity":"6d3c9c9f-2acd-4d74-ad5c-54493af537f8","added_by":"auto","created_at":"2025-10-10 20:19:16","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":4357985,"visible":true,"origin":"","legend":"Article File","description":"","filename":"20250828Fessleretal.MainTextplusExtendedDataFigures.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7483676/v1_covered_0e70b031-33d2-4af7-9585-25e496572a63.pdf"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"Integration of Donor Microbiota Following FMT Predicts Anti–PD-1 Response in Melanoma","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-7483676/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7483676/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Fecal microbiota transplantation (FMT) has shown promise improving anti–PD-1 therapy in melanoma, but the underlying microbial features remain poorly defined. 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