Adaptations and Community Changes in Milk and Water Kefir Microbiomes in Response to Environmental Parameters as Revealed by the Kefir4All Project

Adaptations and Community Changes in Milk and Water Kefir Microbiomes in Response to Environmental Parameters as Revealed by the Kefir4All Project | 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 Adaptations and Community Changes in Milk and Water Kefir Microbiomes in Response to Environmental Parameters as Revealed by the Kefir4All Project Paul Cotter, Liam Walsh, Samuel Breselge, José Martin, Mairead Coakley, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6104343/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Milk and water kefir are fermented beverages prepared by inoculating milk or sugar-rich solutions with kefir grains - containing complex microbial consortia of bacteria and yeast. The increasing global popularity of kefir has driven interest in their microbiomes. Beyond their culinary significance, kefir serves as a model system for studying microbial community assembly, ecological filtering, and evolutionary dynamics. Kefir’s suitability as a model is enhanced by its simplicity (including short fermentation times), adaptability to experimental manipulation, and scalability for both controlled laboratory studies and citizen science initiatives. In this study, we employed genome-resolved metagenomics to investigate milk and water kefir microbiomes, produced over 21 weeks from an initial common source milk or water kefir grain by citizen scientists, using diverse substrates and conditions. Early fermentation (weeks 1–9) was marked by rapid compositional, functional and volatile shifts, leading to reproducible transitions between community states, with values not changing considerably thereafter. At the strain level, we identified multiple coexisting strains within dominant species, with initial fluctuations. While rare environmental species occasionally appeared, they were selectively filtered and did not persist. The sustained coexistence of key species and strains, alongside the emergence of reproducible community types, highlights the resilience and stability of kefir microbiomes across both short- and long-term timeframes. Our findings reinforce kefir’s value as a model for investigating microbial interactions, environmental microbial acquisition, and strain-level dynamics. The co-occurrence patterns observed among specific strains and species provide insight into microbial assembly and persistence, with broader relevance to complex ecosystems such as the gut microbiome. By elucidating patterns of compositional and functional change and assessing how selective pressures shape microbial communities, this study underscores kefir’s utility in microbial ecology and evolution. Earth and environmental sciences/Ecology/Evolutionary ecology Biological sciences/Microbiology/Microbial communities/Metagenomics Biological sciences/Computational biology and bioinformatics/Genome informatics/Genome assembly algorithms citizen science milk kefir water kefir metagenomics lactic acid bacteria identification sequencing Full Text Additional Declarations There is NO Competing Interest. Supplementary Files Supplementaryinformationv8model.pdf Supplementary Information Cite Share Download PDF Status: Under Review 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. 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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-6104343","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":423443386,"identity":"dae8c365-258b-41c7-bacc-3ce8681e3dda","order_by":0,"name":"Paul Cotter","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA9ElEQVRIiWNgGAWjYHACxgMwxgO4WAIBPSAtEjwMDMwGMM1Ea2GTOEBAJRiYs58Bml1jU2fP3vus+kOFnV1//+EHDA8qcGux7MkBajmWJsHDc9zsxoEzyckzbqQZMCScwa3F4ABQC2PDYQkeiTS2GwfbmJMZbgDdmNiGR8v5N1At8s/YCg7+q0+WPw+0IfEfHi034LawsTEcbDhsB7QXqKUBj19mPCs4kHAsTbLnTBqzxJljxxMMgX4BiuDWYs6fvPHBhxobfvb2Y4wfKmqq7eXOH3748EcNHoeBiAQkAbCTDuDWANWCDOzxqR4Fo2AUjIKRCQCmM1SvVKJQdwAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0002-5465-9068","institution":"Teagasc - 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At the strain level, we identified multiple coexisting strains within dominant species, with initial fluctuations. While rare environmental species occasionally appeared, they were selectively filtered and did not persist. The sustained coexistence of key species and strains, alongside the emergence of reproducible community types, highlights the resilience and stability of kefir microbiomes across both short- and long-term timeframes. Our findings reinforce kefir’s value as a model for investigating microbial interactions, environmental microbial acquisition, and strain-level dynamics. The co-occurrence patterns observed among specific strains and species provide insight into microbial assembly and persistence, with broader relevance to complex ecosystems such as the gut microbiome. 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