Functional Remodeling of the Gut Microbiome and Metabolome in Primary Idiopathic Male Infertility

Functional Remodeling of the Gut Microbiome and Metabolome in Primary Idiopathic Male Infertility | 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 Functional Remodeling of the Gut Microbiome and Metabolome in Primary Idiopathic Male Infertility Chen Luo, Hailin Yao, Yang Xian, Tingting Yang, Xiao Xiao, Lijuan Ying, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8785596/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 24 Apr, 2026 Read the published version in BMC Microbiology → Version 1 posted 16 You are reading this latest preprint version Abstract Background Primary idiopathic male infertility (PIMI) is a complex condition with unclear biological mechanisms. Increasing evidence indicates that gut microbiome-derived functional and metabolic alterations can influence host physiological processes, yet microbiome-associated functional changes in PIMI remain poorly characterized. Methods In this case-control study, fecal shotgun metagenomics and untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics were performed in 19 men with PIMI and 12 fertile controls, alongside computer-assisted semen analysis. The study workflow integrated differential analyses, correlation analyses among key microbial species, metabolites, and clinical traits, and Random Forest modeling to derive a microbial-metabolic panel. Results Compared with fertile controls, infertile men exhibited selective functional remodeling of gut microbial pathways and fecal metabolic profiles, accompanied by reduced sperm concentration and progressive motility and increased round cell counts. Although overall microbial diversity was broadly comparable between groups, 23 differentially abundant species and 53 altered Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified by metagenomic profiling. Untargeted metabolomics annotated 4,434 metabolites and identified 780 differential metabolites, with enrichment of 29 KEGG pathways. Eight key microbial species and eight key metabolites mapped to sperm- and testis-related pathways showed coordinated correlations with semen parameters. An integrated Random Forest model incorporating microbial and metabolic features demonstrated robust discrimination between infertile and fertile men, with optimal performance achieved using six top-ranked features. Conclusions PIMI is associated with selective gut microbial functional shifts and fecal metabolic disturbances that correlate with semen quality. Multi-omics integration highlights coordinated microbiome-metabolome alterations, providing insights into host-associated microbial functional dysregulation in male infertility. Primary idiopathic male infertility Gut microbiome metabolome Shotgun metagenomics Untargeted metabolomics Full Text Additional Declarations No competing interests reported. Table 1 is available in the Supplementary Files section. Supplementary Files Table1.docx TableS1.xlsx TableS2.xlsx TableS3.xlsx Cite Share Download PDF Status: Published Journal Publication published 24 Apr, 2026 Read the published version in BMC Microbiology → Version 1 posted Editorial decision: Revision requested 09 Mar, 2026 Reviews received at journal 06 Mar, 2026 Reviews received at journal 04 Mar, 2026 Reviewers agreed at journal 03 Mar, 2026 Reviewers agreed at journal 03 Mar, 2026 Reviews received at journal 02 Mar, 2026 Reviewers agreed at journal 02 Mar, 2026 Reviewers agreed at journal 01 Mar, 2026 Reviewers agreed at journal 28 Feb, 2026 Reviewers agreed at journal 28 Feb, 2026 Reviewers agreed at journal 27 Feb, 2026 Reviewers invited by journal 27 Feb, 2026 Editor assigned by journal 26 Feb, 2026 Editor invited by journal 14 Feb, 2026 Submission checks completed at journal 13 Feb, 2026 First submitted to journal 13 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. 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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-8785596","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":600179884,"identity":"d4be5102-f1e3-4d3a-8808-fd04a43fff38","order_by":0,"name":"Chen Luo","email":"","orcid":"","institution":"Sichuan University","correspondingAuthor":false,"prefix":"","firstName":"Chen","middleName":"","lastName":"Luo","suffix":""},{"id":600179887,"identity":"ff074888-9182-4dc0-8fa1-7998e51ec1f7","order_by":1,"name":"Hailin Yao","email":"","orcid":"","institution":"Sichuan 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Increasing evidence indicates that gut microbiome-derived functional and metabolic alterations can influence host physiological processes, yet microbiome-associated functional changes in PIMI remain poorly characterized.\u003c/p\u003e\u003ch2\u003eMethods\u003c/h2\u003e \u003cp\u003eIn this case-control study, fecal shotgun metagenomics and untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics were performed in 19 men with PIMI and 12 fertile controls, alongside computer-assisted semen analysis. The study workflow integrated differential analyses, correlation analyses among key microbial species, metabolites, and clinical traits, and Random Forest modeling to derive a microbial-metabolic panel.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eCompared with fertile controls, infertile men exhibited selective functional remodeling of gut microbial pathways and fecal metabolic profiles, accompanied by reduced sperm concentration and progressive motility and increased round cell counts. Although overall microbial diversity was broadly comparable between groups, 23 differentially abundant species and 53 altered Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified by metagenomic profiling. Untargeted metabolomics annotated 4,434 metabolites and identified 780 differential metabolites, with enrichment of 29 KEGG pathways. Eight key microbial species and eight key metabolites mapped to sperm- and testis-related pathways showed coordinated correlations with semen parameters. An integrated Random Forest model incorporating microbial and metabolic features demonstrated robust discrimination between infertile and fertile men, with optimal performance achieved using six top-ranked features.\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e \u003cp\u003ePIMI is associated with selective gut microbial functional shifts and fecal metabolic disturbances that correlate with semen quality. Multi-omics integration highlights coordinated microbiome-metabolome alterations, providing insights into host-associated microbial functional dysregulation in male infertility.\u003c/p\u003e","manuscriptTitle":"Functional Remodeling of the Gut Microbiome and Metabolome in Primary Idiopathic Male Infertility","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-04 22:57:33","doi":"10.21203/rs.3.rs-8785596/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-03-09T16:10:26+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-03-06T15:09:34+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-03-04T14:40:34+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"217617957100036707474960516319376273594","date":"2026-03-03T10:54:43+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"69099962107542112374306783505036624588","date":"2026-03-03T07:19:12+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-03-02T16:18:24+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"60350381674005028544645665814449333339","date":"2026-03-02T12:16:23+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"99185228434526220947322680816714469266","date":"2026-03-01T20:45:27+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"237804168211670601191072223304946302416","date":"2026-02-28T22:51:04+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"636789256539709524121319842963653767","date":"2026-02-28T14:07:29+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"126355220322427726776210749783500063600","date":"2026-02-27T16:30:01+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-02-27T15:17:12+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-02-26T09:22:01+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2026-02-14T05:34:41+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-02-14T04:55:48+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Microbiology","date":"2026-02-14T04:51:31+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-microbiology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"mcro","sideBox":"Learn more about [BMC Microbiology](http://bmcmicrobiol.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/mcro","title":"BMC Microbiology","twitterHandle":"#bmcmicrobiology","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"cdd0c6f5-b4f3-4724-a63f-ec4511b65fc1","owner":[],"postedDate":"March 4th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2026-04-27T16:04:34+00:00","versionOfRecord":{"articleIdentity":"rs-8785596","link":"https://doi.org/10.1186/s12866-026-05064-x","journal":{"identity":"bmc-microbiology","isVorOnly":false,"title":"BMC Microbiology"},"publishedOn":"2026-04-24 15:58:51","publishedOnDateReadable":"April 24th, 2026"},"versionCreatedAt":"2026-03-04 22:57:33","video":"","vorDoi":"10.1186/s12866-026-05064-x","vorDoiUrl":"https://doi.org/10.1186/s12866-026-05064-x","workflowStages":[]},"version":"v1","identity":"rs-8785596","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8785596","identity":"rs-8785596","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}