Comparative Genomic and Phenotypic Profiling of Commercial Probiotic Enterococcus faecium Strains: Insights into Safety and Functional Attributes

Comparative Genomic and Phenotypic Profiling of Commercial Probiotic Enterococcus faecium Strains: Insights into Safety and Functional Attributes | 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 Comparative Genomic and Phenotypic Profiling of Commercial Probiotic Enterococcus faecium Strains: Insights into Safety and Functional Attributes Yongqi Gan, Manman Lu, Lanyan Fan, Jun Nong, Pingping Shangguan, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9098916/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 10 You are reading this latest preprint version Abstract Enterococcus faecium is widely used in probiotics but can also act as an opportunistic pathogen, necessitating strain-specific safety and efficacy assessments. This study conducted a comparative genomic and phenotypic analysis of five E. faecium strains isolated from commercial probiotic products alongside five reference strains. Whole-genome sequencing revealed that the probiotic-derived strains clustered into two distinct phylogenetic clades (Clade I: ST-812; Clade II: ST-76), corroborated by Average Nucleotide Identity and Multilocus Sequence Typing analyses. These clades exhibited coherent functional genomic profiles, with Clade I enriched in genes for carbohydrate metabolism and dietary fiber degradation, while Clade II showed a different emphasis, including carotenoid biosynthesis. Crucially, all probiotic strains lacked high-risk antibiotic resistance genes ( vanA ) and major virulence determinants ( esp , hyl , gelE ) found in the clinical control strain ATCC 51559, and were phenotypically susceptible to key antibiotics. In vitro probiotic property assays further demonstrated significant inter-strain variability in gastric acid tolerance, bile salt resistance, and bile salt hydrolase activity, underscoring the strain-specific nature of functional performance. Our integrated analysis establishes a robust link between genomic identity, functional potential, and safety profile in commercial E. faecium probiotics. This study provides a comprehensive genomic framework for strain-level safety assessment and supports the informed selection of E. faecium strains for probiotic applications. Enterococcus faecium probiotics comparative genomics whole-genome sequencing safety assessment Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Under Review Version 1 posted Reviews received at journal 06 May, 2026 Reviews received at journal 04 May, 2026 Reviewers agreed at journal 03 May, 2026 Reviews received at journal 19 Apr, 2026 Reviewers agreed at journal 09 Apr, 2026 Reviewers agreed at journal 07 Apr, 2026 Reviewers invited by journal 07 Apr, 2026 Editor assigned by journal 12 Mar, 2026 Submission checks completed at journal 12 Mar, 2026 First submitted to journal 11 Mar, 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. 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-9098916","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":620503817,"identity":"065f1d5c-f990-4c76-a04f-473d7a97d459","order_by":0,"name":"Yongqi Gan","email":"","orcid":"","institution":"Guangxi Institute for Drug Control","correspondingAuthor":false,"prefix":"","firstName":"Yongqi","middleName":"","lastName":"Gan","suffix":""},{"id":620503819,"identity":"26b44998-8feb-4bf4-a5f7-e359086031d1","order_by":1,"name":"Manman Lu","email":"","orcid":"","institution":"Guangxi Academy of Agricultural 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