Flavor development in melon and bitter gourd: roles of endophytic microbiome and metabolome

Flavor development in melon and bitter gourd: roles of endophytic microbiome and metabolome | 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 Flavor development in melon and bitter gourd: roles of endophytic microbiome and metabolome Xinni Li, Da Yang, Liyuan Liao, Kexin Lu, Haidong Huang, Shangdong Yang This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9342179/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 Endophytic microbiome and metabolome are known to influence plant physiology, but their specific roles in fruit flavor development remain poorly understood. To explore microbial and metabolic factors linked to distinct flavor phenotypes, we compared stem endophytic microbiome composition and untargeted metabolomes between melon ( Cucumis melo , CM) and bitter gourd ( Momordica charantia , MC). Our goal was to identify candidate taxa, metabolites and pathways potentially related to sweetness and bitterness. Results showed that fungal diversity and richness were significantly higher in CM than in MC. CM stems were characterized by enrichment of Ascomycota and unique dominance of Sphingomonas , whereas MC exhibited significant enrichment of Botryosporium and a higher relative abundance of Bacteroidota. Metabolomic and pathway analyses revealed that CM displayed upregulation of phenylalanine, tyrosine and tryptophan biosynthesis, flavonoid biosynthesis, and cofactor biosynthesis, along with accumulation of sweet-enhancing metabolites such as naringin dihydrochalcone. By contrast, MC showed elevated activity in plant hormone signal transduction and higher levels of (S)-abscisic acid and dihydrozeatin. This study demonstrates distinct stem endophytic microbiomes and metabolomes between melon and bitter gourd, and highlights candidate functional microorganisms, key metabolites and metabolic pathways that correlate with sweetness and bitterness phenotypes. Further experimental validation is needed to confirm the causal roles of these candidates. These findings provide new insights into the mechanisms underlying melon sweetness and bitter gourd bitterness, and lay a methodological foundation for multi-omics investigations and the future development of microbiome- or metabolite-based strategies for modulating fruit quality and flavor. Melon Bitter gourd Endophytic microbes Metabolites Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementaryMaterial1.docx 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-9342179","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":627269479,"identity":"8163002d-e051-407b-8827-5a40decde412","order_by":0,"name":"Xinni Li","email":"","orcid":"","institution":"Guangxi University","correspondingAuthor":false,"prefix":"","firstName":"Xinni","middleName":"","lastName":"Li","suffix":""},{"id":627269480,"identity":"3eefe0cd-ae9b-402d-890c-fa8a8c0de7e8","order_by":1,"name":"Da Yang","email":"","orcid":"","institution":"Guangxi 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To explore microbial and metabolic factors linked to distinct flavor phenotypes, we compared stem endophytic microbiome composition and untargeted metabolomes between melon (\u003cem\u003eCucumis melo\u003c/em\u003e, CM) and bitter gourd (\u003cem\u003eMomordica charantia\u003c/em\u003e, MC). Our goal was to identify candidate taxa, metabolites and pathways potentially related to sweetness and bitterness. Results showed that fungal diversity and richness were significantly higher in CM than in MC. CM stems were characterized by enrichment of Ascomycota and unique dominance of \u003cem\u003eSphingomonas\u003c/em\u003e, whereas MC exhibited significant enrichment of \u003cem\u003eBotryosporium\u003c/em\u003e and a higher relative abundance of Bacteroidota. Metabolomic and pathway analyses revealed that CM displayed upregulation of phenylalanine, tyrosine and tryptophan biosynthesis, flavonoid biosynthesis, and cofactor biosynthesis, along with accumulation of sweet-enhancing metabolites such as naringin dihydrochalcone. By contrast, MC showed elevated activity in plant hormone signal transduction and higher levels of (S)-abscisic acid and dihydrozeatin. This study demonstrates distinct stem endophytic microbiomes and metabolomes between melon and bitter gourd, and highlights candidate functional microorganisms, key metabolites and metabolic pathways that correlate with sweetness and bitterness phenotypes. Further experimental validation is needed to confirm the causal roles of these candidates. 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