Nutritional gradients orchestrate spatiotemporal microbial assembly and adaptive evolution in the neonatal mammalian gut

Nutritional gradients orchestrate spatiotemporal microbial assembly and adaptive evolution in the neonatal mammalian 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 Research Article Nutritional gradients orchestrate spatiotemporal microbial assembly and adaptive evolution in the neonatal mammalian gut Di Yin, Yunlong Gao, Jiaqi Zhao, Tao Zhang, Pengchao Zhan, Yueying Yu, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7903532/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 9 You are reading this latest preprint version Abstract Nutritional cues during early life play a pivotal role in shaping the gastrointestinal microbiome, yet the evolutionary forces governing this process remain poorly understood. Using neonatal calves as a mammalian model, we established a genome-resolved catalog encompassing 386 closed genomes and 2,147 species-level genome bins, markedly expanding available resources. Microbial communities displayed a three-stage developmental trajectory, with deterministic selection dominating in the stomach and hindgut, while stochastic drift was more evident in the small intestine. Genome-wide single-nucleotide variant analyses revealed pervasive positive selection on carbohydrate-active pathways. Functional validation demonstrated that variants of E. coli lacZ and Cryptobacteroides sp900316045 bglB-4 exhibited altered enzymatic activities, consistent with adaptive responses to nutritional shifts. Comparative genomics further uncovered age-dependent divergence among coexisting Prevotella species, reflecting niche specialization between milk-adapted and fiber-adapted lineages. Together, these findings provide a mechanistic framework for how nutritional gradients orchestrate spatiotemporal assembly and microevolution of the neonatal gut microbiome, and deliver a broadly applicable genomic resource for exploring microbial adaptation across mammalian hosts. Positive selection Age-dependent divergence Genome-resolved catalog Deterministic selection Enzymatic activity alteration Full Text Additional Declarations No competing interests reported. Supplementary Files Additionalfile1.xlsx Additionalfile2.xlsx Additionalfile3.xlsx Additionalfile4.xlsx Additionalfile5.xlsx Additionalfile6.xlsx Additionalfile7.xlsx Additionalfile8.xlsx Additionalfile9.xlsx Additionalfile10.xlsx Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 26 Feb, 2026 Reviews received at journal 13 Feb, 2026 Reviews received at journal 06 Feb, 2026 Reviewers agreed at journal 05 Feb, 2026 Reviewers agreed at journal 03 Feb, 2026 Reviewers invited by journal 02 Feb, 2026 Editor assigned by journal 27 Oct, 2025 Submission checks completed at journal 20 Oct, 2025 First submitted to journal 20 Oct, 2025 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-7903532","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":584826075,"identity":"4e6564be-93af-431e-8099-096cf98f9f01","order_by":0,"name":"Di Yin","email":"","orcid":"","institution":"Nanjing Agricultural University","correspondingAuthor":false,"prefix":"","firstName":"Di","middleName":"","lastName":"Yin","suffix":""},{"id":584826076,"identity":"343fdd10-eea8-4394-ba3a-e3aadc7e8a5d","order_by":1,"name":"Yunlong Gao","email":"","orcid":"","institution":"Nanjing Agricultural 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