BacTaxID: A universal framework for standardized bacterial typing

BacTaxID: A universal framework for standardized bacterial typing | 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 BacTaxID: A universal framework for standardized bacterial typing Val Lanza, Miguel Diez Fernández de Bobadilla This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8935510/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 Bacterial strain typing is key to surveillance, outbreak investigation and microbial ecology, yet current systems remain species-specific, reference-dependent and lack a universal, interpretable metric of genomic relatedness. Here, we introduce BacTaxID, a fully configurable, whole-genome k‑mer-based framework that encodes each genome as a numeric sketch and organizes strains into hierarchical clusters with user‑defined similarity thresholds. BacTaxID distances are strictly proportional to Average Nucleotide Identity (ANI), providing a direct quantitative link between vectorial typing and genome-wide divergence. Applied to 2.3 million genomes from “All the Bacteria” database across 67 genera, BacTaxID demonstrates universal concordance species and sub-species classification systems, while capturing finer strain-level diversity than traditional reference-based approaches. In simulated surveillance and real outbreak datasets, BacTaxID reproduces SNP and cgMLST-based definitions while enabling rapid, scalable screening. Precomputed genus-level schemes and an open implementation provide a practical, genus‑agnostic alternative to classical typing systems for standardized bacterial classification. Biological sciences/Computational biology and bioinformatics/Classification and taxonomy Biological sciences/Microbiology/Microbial genetics Biological sciences/Computational biology and bioinformatics/Software Full Text Additional Declarations There is NO Competing Interest. 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. 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-8935510","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":595773221,"identity":"d5d3eab6-c22a-4d70-8866-b555114bd97f","order_by":0,"name":"Val Lanza","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABD0lEQVRIiWNgGAWjYFAC5oYPEEYCiJCTA5EHHuDVwtg4A0mLsTFYSwIpWhIb4GwcwOD4wcaGj3vuyJuzJx/+wNhmkD4/7PBDoC12croNOLScSWxsnPHsmeHOnmcJBkAtuRtvpxkAtSQbmx3ArkWyIbH9Mc+Bw4wbbuQYJDCc+ZO7cXYCSMuBxG24tPQ/bGz+c+Cw/YYb+R8OMJwxSDecnf4BrxZ+icTGZoYDhxOBtjA2MFQYJMhL5+C3hV/iYWNjz4HDyRvOPDNmSKgwMNwgnVNwIMEAt1/Y+JMPNvw4cNh2w/Hkxx8+GBjIy89O3/zhQ4WdHC4tqCABiA3AKg2IUQ4D8g2kqB4Fo2AUjIKRAADBKGy03JJSnwAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0003-0870-9500","institution":"Ramón y Cajal Health Research Institute (IRYCIS)","correspondingAuthor":true,"prefix":"","firstName":"Val","middleName":"","lastName":"Lanza","suffix":""},{"id":595773222,"identity":"5b70bd8c-724d-462d-8327-deb4eca82d0a","order_by":1,"name":"Miguel Diez Fernández de Bobadilla","email":"","orcid":"","institution":"Institute of Functional Biology and Genomics, CSIC \u0026 University of Salamanca","correspondingAuthor":false,"prefix":"","firstName":"Miguel","middleName":"Diez Fernández","lastName":"de Bobadilla","suffix":""}],"badges":[],"createdAt":"2026-02-21 20:00:09","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8935510/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8935510/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":104781371,"identity":"b9bbdf52-8cbe-4701-874e-c5a6c2b4a74e","added_by":"auto","created_at":"2026-03-17 07:55:33","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1219659,"visible":true,"origin":"","legend":"Article File","description":"","filename":"BacTaxIDmanuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8935510/v1_covered_18c41786-11a2-4e5b-b428-dd91e6b541ae.pdf"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"BacTaxID: A universal framework for standardized bacterial typing","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-8935510/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8935510/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Bacterial strain typing is key to surveillance, outbreak investigation and microbial ecology, yet current systems remain species-specific, reference-dependent and lack a universal, interpretable metric of genomic relatedness. 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