Genome-level Constraint-Based Analysis of Megasphaera sp. MJR8396C Reveals Dual Metabolic Roles in the Human Gut

Genome-level Constraint-Based Analysis of Megasphaera sp. MJR8396C Reveals Dual Metabolic Roles in the Human Gut | 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 Genome-level Constraint-Based Analysis of Megasphaera sp. MJR8396C Reveals Dual Metabolic Roles in the Human Gut Andrea Dell’Olio, Joy Iheoma van Geerestein, Josep Rubert, William T. Scott Jr This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7827579/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 Understanding the metabolic behavior of gut bacteria is crucial for developing targeted microbiome-based interventions in obesity. In this study, we investigated the metabolic flexibility of Megasphaera sp. MJR8396C , an understudied gut microbe implicated in altered microbiota functionality, using constraint-based reconstruction and analysis (COBRA). Our findings demonstrate that COBRA, combined with flux balance analysis (FBA), offers a comprehensive framework to elucidate microbial metabolism under diverse nutritional environments. We reveal that the metabolic outputs of Megasphaera sp. MJR8396C significantly vary depending on nutrient availability, genetic interventions, and microbial community context. Specifically, Megasphaera sp. MJR8396C can engage in Stickland-type amino acid fermentation and produce both beneficial metabolites such as butyrate, and potentially harmful by-products like ammonia. The ambiguous role of this bacterium—being beneficial or detrimental in obesity—is context-dependent, emphasizing the importance of metabolic environment modulation. We further show that computational tools such as OptForce and co-culture modeling can guide real-time interventions, including genetic modifications or community adjustments, to optimize bacterial metabolic profiles. These results highlight the potential of systems biology approaches to address knowledge gaps and strategically harness gut microbes for therapeutic outcomes. Biological sciences/Biotechnology Biological sciences/Computational biology and bioinformatics Biological sciences/Microbiology genome-scale metabolic model Megasphaera sp. MJR8396C flux balance analysis Stickland metabolism Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementaryMaterialManuscript.pdf 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-7827579","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":542375295,"identity":"2e2fba12-9631-4771-8fb2-fb792be759c5","order_by":0,"name":"Andrea Dell’Olio","email":"","orcid":"","institution":"Wageningen University \u0026 Research, Food Quality \u0026 Design Group","correspondingAuthor":false,"prefix":"","firstName":"Andrea","middleName":"","lastName":"Dell’Olio","suffix":""},{"id":542375296,"identity":"eb967798-fc94-4dfc-ac36-d9549db400fd","order_by":1,"name":"Joy Iheoma van Geerestein","email":"","orcid":"","institution":"Wageningen University \u0026 Research, Food Quality \u0026 Design Group","correspondingAuthor":false,"prefix":"","firstName":"Joy","middleName":"Iheoma van","lastName":"Geerestein","suffix":""},{"id":542375297,"identity":"8abacb4b-734e-4c09-b240-5aa7cc2084ce","order_by":2,"name":"Josep Rubert","email":"","orcid":"","institution":"Wageningen University \u0026 Research, Food Quality \u0026 Design Group","correspondingAuthor":false,"prefix":"","firstName":"Josep","middleName":"","lastName":"Rubert","suffix":""},{"id":542375298,"identity":"6f0e8e30-1f4c-4fe6-999b-d32f5afa08ff","order_by":3,"name":"William T. 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MJR8396C Reveals Dual Metabolic Roles in the Human Gut","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":"genome-scale metabolic model, Megasphaera sp. MJR8396C, flux balance analysis, Stickland metabolism","lastPublishedDoi":"10.21203/rs.3.rs-7827579/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7827579/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eUnderstanding the metabolic behavior of gut bacteria is crucial for developing targeted microbiome-based interventions in obesity. In this study, we investigated the metabolic flexibility of \u003cem\u003eMegasphaera sp. MJR8396C\u003c/em\u003e, an understudied gut microbe implicated in altered microbiota functionality, using constraint-based reconstruction and analysis (COBRA). Our findings demonstrate that COBRA, combined with flux balance analysis (FBA), offers a comprehensive framework to elucidate microbial metabolism under diverse nutritional environments. We reveal that the metabolic outputs of \u003cem\u003eMegasphaera sp. MJR8396C\u003c/em\u003e significantly vary depending on nutrient availability, genetic interventions, and microbial community context. Specifically, \u003cem\u003eMegasphaera sp. MJR8396C\u003c/em\u003e can engage in Stickland-type amino acid fermentation and produce both beneficial metabolites such as butyrate, and potentially harmful by-products like ammonia. The ambiguous role of this bacterium\u0026mdash;being beneficial or detrimental in obesity\u0026mdash;is context-dependent, emphasizing the importance of metabolic environment modulation. We further show that computational tools such as OptForce and co-culture modeling can guide real-time interventions, including genetic modifications or community adjustments, to optimize bacterial metabolic profiles. These results highlight the potential of systems biology approaches to address knowledge gaps and strategically harness gut microbes for therapeutic outcomes.\u003c/p\u003e","manuscriptTitle":"Genome-level Constraint-Based Analysis of Megasphaera sp. MJR8396C Reveals Dual Metabolic Roles in the Human Gut","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-11-11 19:53:08","doi":"10.21203/rs.3.rs-7827579/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":"e9dfe4d5-040f-4794-970a-a1044a6c8c99","owner":[],"postedDate":"November 11th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":57694382,"name":"Biological sciences/Biotechnology"},{"id":57694383,"name":"Biological sciences/Computational biology and bioinformatics"},{"id":57694384,"name":"Biological sciences/Microbiology"}],"tags":[],"updatedAt":"2025-12-09T06:09:01+00:00","versionOfRecord":[],"versionCreatedAt":"2025-11-11 19:53:08","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7827579","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7827579","identity":"rs-7827579","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}