Gut Microbiota Protects Against Liver Injury and Fibrosis via Activation of the CYP Eicosanoid Pathway

Gut Microbiota Protects Against Liver Injury and Fibrosis via Activation of the CYP Eicosanoid Pathway | 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 Article Gut Microbiota Protects Against Liver Injury and Fibrosis via Activation of the CYP Eicosanoid Pathway Guodong Zhang, Quancai Sun, Jing Sun, Nan Jing, Matthew Edin, and 15 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6356145/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 Gut microbiota has been shown to play an important role in the pathogenesis of liver injury and fibrosis, but the specific microbial factors or pathways involved remain poorly defined. Here we show that specific gut microbial metabolites, notably indole, activate the cytochrome P450 (CYP) eicosanoid pathway in the liver and protect the liver against liver injury and fibrosis. Using LC-MS/MS-based lipidomics to compare conventionally raised mice with germ-free or antibiotic-treated mice, we show that the gut microbiota induces the CYP eicosanoid pathway in the liver. Furthermore, by administering exogenous indole or mono-colonizing germ-free mice with indole-producing Bacteroides thetaiotaomicron or a mutant strain lacking indole production, we demonstrate that gut bacteria-produced indole activates the liver’s CYP eicosanoid pathway through pregnane X receptor-dependent mechanisms. Finally, we find that disruption of the microbiota-liver-CYP axis, through inhibition or genetic ablation of CYP monooxygenases, or antibiotic suppression of gut microbiota, exacerbates chemically or surgically induced liver injury or fibrosis. Conversely, activation of this axis through indole administration attenuates liver injury and fibrosis. Together, these results demonstrate that the microbiota-liver-CYP axis plays a key role in the mechanisms by which gut microbiota interacts with the liver to influence host metabolism and disease progression. Health sciences/Gastroenterology/Hepatology/Liver diseases/Hepatotoxicity Biological sciences/Biological techniques/Metabolomics Health sciences/Gastroenterology/Gastrointestinal system/Microbiota Gut-liver axis eicosanoids liver injury liver fibrosis lipidomics indole Full Text Additional Declarations There is NO Competing Interest. 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-6356145","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":437496728,"identity":"2c1c4824-10d2-48f2-9f78-4a4378316eef","order_by":0,"name":"Guodong Zhang","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA5ElEQVRIiWNgGAWjYFCCBDYQKQfEBmAEFCFOizHpWhIboOoJa5F3T3/24OeO2vQNxw9v/MxTUMfAz55jgFeL4ZkH6Ya9Z47nbjiTVizNY3CYQbLnDQEtMxKOSfC2HcvdcIPHQHKGwQEGgxuEbJmR2Cb5t+1YusENHuOfMwzqGOwJaZGXSGaT5m2rSQBqMZP4YMDMYCBBQIsBzzM2adm2A4Yzz6SVWXwwOMwjceZZAX5b2tOfSb5tq5PnO354842EP3Vy/O3JG/DbcgBMHYYL8OBVDralAUzVEVQ4CkbBKBgFIxgAABtVSKl6jGwHAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0001-7780-5470","institution":"University of California Davis","correspondingAuthor":true,"prefix":"","firstName":"Guodong","middleName":"","lastName":"Zhang","suffix":""},{"id":437496729,"identity":"13ef95c0-1450-4bcf-a854-29681c5fb9b7","order_by":1,"name":"Quancai Sun","email":"","orcid":"https://orcid.org/0000-0002-9171-269X","institution":"Florida state University","correspondingAuthor":false,"prefix":"","firstName":"Quancai","middleName":"","lastName":"Sun","suffix":""},{"id":437496730,"identity":"b55a3efa-5f1d-4c8c-945b-9598edfece2f","order_by":2,"name":"Jing Sun","email":"","orcid":"","institution":"China Agricultural University","correspondingAuthor":false,"prefix":"","firstName":"Jing","middleName":"","lastName":"Sun","suffix":""},{"id":437496731,"identity":"1f4595e6-7a78-42ce-8771-1da8097fabdd","order_by":3,"name":"Nan Jing","email":"","orcid":"","institution":"University of California Davis","correspondingAuthor":false,"prefix":"","firstName":"Nan","middleName":"","lastName":"Jing","suffix":""},{"id":437496732,"identity":"226df92e-b1d5-48ad-adfa-53c899c5dea1","order_by":4,"name":"Matthew Edin","email":"","orcid":"","institution":"National Institute of Environmental Health Sciences","correspondingAuthor":false,"prefix":"","firstName":"Matthew","middleName":"","lastName":"Edin","suffix":""},{"id":437496733,"identity":"62537e81-0ce6-4045-b673-b4156246648b","order_by":5,"name":"Yige Wang","email":"","orcid":"","institution":"University of California, Davis","correspondingAuthor":false,"prefix":"","firstName":"Yige","middleName":"","lastName":"Wang","suffix":""},{"id":437496734,"identity":"39ac8ff0-b8d7-4690-bbd7-0c813f8e9cbc","order_by":6,"name":"Weidong Xu","email":"","orcid":"","institution":"Jiangsu University","correspondingAuthor":false,"prefix":"","firstName":"Weidong","middleName":"","lastName":"Xu","suffix":""},{"id":437496735,"identity":"b7c5c66e-bedc-4953-9a83-ca9105539f35","order_by":7,"name":"Jianan Zhang","email":"","orcid":"","institution":"University of Massachusetts, Amherst","correspondingAuthor":false,"prefix":"","firstName":"Jianan","middleName":"","lastName":"Zhang","suffix":""},{"id":437496736,"identity":"b8e2050a-0c30-4045-a039-719dd7089f90","order_by":8,"name":"Weicang Wang","email":"","orcid":"","institution":"Purdue University","correspondingAuthor":false,"prefix":"","firstName":"Weicang","middleName":"","lastName":"Wang","suffix":""},{"id":437496737,"identity":"7e02c36a-38ce-45e1-b032-71777ca08776","order_by":9,"name":"Fred Lih","email":"","orcid":"https://orcid.org/0000-0002-2260-816X","institution":"Division of Intramural Research, National Institute for Environmental Health Sciences, National Institutes of Health","correspondingAuthor":false,"prefix":"","firstName":"Fred","middleName":"","lastName":"Lih","suffix":""},{"id":437496738,"identity":"6261d979-dbe7-4bc3-8be9-a9576aa30bc6","order_by":10,"name":"Weimin Wang","email":"","orcid":"","institution":"China Agricultural University","correspondingAuthor":false,"prefix":"","firstName":"Weimin","middleName":"","lastName":"Wang","suffix":""},{"id":437496739,"identity":"da9314c1-a11d-4d0c-84ce-6e95d516f971","order_by":11,"name":"Vladimir Yeliseyev","email":"","orcid":"","institution":"Brigham and Women's Hospital, Boston","correspondingAuthor":false,"prefix":"","firstName":"Vladimir","middleName":"","lastName":"Yeliseyev","suffix":""},{"id":437496740,"identity":"2bfcb8cc-c8e4-42fc-9502-b79f83c024be","order_by":12,"name":"Jie Lin","email":"","orcid":"","institution":"Florida State University","correspondingAuthor":false,"prefix":"","firstName":"Jie","middleName":"","lastName":"Lin","suffix":""},{"id":437496741,"identity":"6933f6c1-e3b1-47de-aa53-431e33780e09","order_by":13,"name":"You-Tae Kim","email":"","orcid":"","institution":"University of California, Davis","correspondingAuthor":false,"prefix":"","firstName":"You-Tae","middleName":"","lastName":"Kim","suffix":""},{"id":437496742,"identity":"ba3354d2-a53f-4ae4-95ce-c47b6fbd1114","order_by":14,"name":"Renhua Song","email":"","orcid":"https://orcid.org/0000-0002-8228-7281","institution":"Centenary Institute","correspondingAuthor":false,"prefix":"","firstName":"Renhua","middleName":"","lastName":"Song","suffix":""},{"id":437496743,"identity":"fa633e0a-9326-41e5-b525-cd8e744a2892","order_by":15,"name":"Sven Pettersson","email":"","orcid":"https://orcid.org/0000-0001-8903-3738","institution":"National University of Singapore","correspondingAuthor":false,"prefix":"","firstName":"Sven","middleName":"","lastName":"Pettersson","suffix":""},{"id":437496744,"identity":"1a890c93-d5da-4cb1-a94e-13f8f8a41017","order_by":16,"name":"Justin Wong","email":"","orcid":"https://orcid.org/0000-0002-7038-5079","institution":"University of Sydney","correspondingAuthor":false,"prefix":"","firstName":"Justin","middleName":"","lastName":"Wong","suffix":""},{"id":437496745,"identity":"3802677b-e7b2-4b6f-8219-70e0333af61d","order_by":17,"name":"David Mills","email":"","orcid":"","institution":"University of California, Davis","correspondingAuthor":false,"prefix":"","firstName":"David","middleName":"","lastName":"Mills","suffix":""},{"id":437496746,"identity":"3161c537-582e-4071-be51-001f32efe3ca","order_by":18,"name":"Darryl Zeldin","email":"","orcid":"","institution":"NIH/NIEHS","correspondingAuthor":false,"prefix":"","firstName":"Darryl","middleName":"","lastName":"Zeldin","suffix":""},{"id":437496747,"identity":"b22f85e1-5c58-4bce-8ec2-d4b176349775","order_by":19,"name":"Haixia Yang","email":"","orcid":"","institution":"China Agricultural University","correspondingAuthor":false,"prefix":"","firstName":"Haixia","middleName":"","lastName":"Yang","suffix":""}],"badges":[],"createdAt":"2025-04-01 22:10:37","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6356145/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6356145/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":80240071,"identity":"e01da9dd-8fb6-4c70-8d96-8570b123b0b7","added_by":"auto","created_at":"2025-04-09 14:39:07","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":7009647,"visible":true,"origin":"","legend":"Article File","description":"","filename":"NatComm2025.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6356145/v1_covered_c4831d1a-e031-4c07-baa1-16dc3a9c6df9.pdf"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"Gut Microbiota Protects Against Liver Injury and Fibrosis via Activation of the CYP Eicosanoid Pathway","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"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":"Gut-liver axis, eicosanoids, liver injury, liver fibrosis, lipidomics, indole","lastPublishedDoi":"10.21203/rs.3.rs-6356145/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6356145/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Gut microbiota has been shown to play an important role in the pathogenesis of liver injury and fibrosis, but the specific microbial factors or pathways involved remain poorly defined. Here we show that specific gut microbial metabolites, notably indole, activate the cytochrome P450 (CYP) eicosanoid pathway in the liver and protect the liver against liver injury and fibrosis. Using LC-MS/MS-based lipidomics to compare conventionally raised mice with germ-free or antibiotic-treated mice, we show that the gut microbiota induces the CYP eicosanoid pathway in the liver. Furthermore, by administering exogenous indole or mono-colonizing germ-free mice with indole-producing Bacteroides thetaiotaomicron or a mutant strain lacking indole production, we demonstrate that gut bacteria-produced indole activates the liver’s CYP eicosanoid pathway through pregnane X receptor-dependent mechanisms. Finally, we find that disruption of the microbiota-liver-CYP axis, through inhibition or genetic ablation of CYP monooxygenases, or antibiotic suppression of gut microbiota, exacerbates chemically or surgically induced liver injury or fibrosis. Conversely, activation of this axis through indole administration attenuates liver injury and fibrosis. Together, these results demonstrate that the microbiota-liver-CYP axis plays a key role in the mechanisms by which gut microbiota interacts with the liver to influence host metabolism and disease progression.","manuscriptTitle":"Gut Microbiota Protects Against Liver Injury and Fibrosis via Activation of the CYP Eicosanoid Pathway","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-04-03 04:08:56","doi":"10.21203/rs.3.rs-6356145/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":"600c44c6-cb8e-463b-9626-1d37b028bd4d","owner":[],"postedDate":"April 3rd, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":46585341,"name":"Health sciences/Gastroenterology/Hepatology/Liver diseases/Hepatotoxicity"},{"id":46585342,"name":"Biological sciences/Biological techniques/Metabolomics"},{"id":46585343,"name":"Health sciences/Gastroenterology/Gastrointestinal system/Microbiota"}],"tags":[],"updatedAt":"2025-06-27T05:53:21+00:00","versionOfRecord":[],"versionCreatedAt":"2025-04-03 04:08:56","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-6356145","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6356145","identity":"rs-6356145","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}