{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T00:53:05Z","timestamp":1793321585503,"version":"4.5.0"},"posted":{"date-parts":[[2024,3,11]]},"group-title":"Bioinformatics","reference-count":89,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2024,3,11]],"date-time":"2024-03-11T00:00:00Z","timestamp":1710115200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["220540\/Z\/20\/A"],"award-info":[{"award-number":["220540\/Z\/20\/A"]}],"id":[{"id":"https:\/\/ror.org\/029chgv08","id-type":"ROR","asserted-by":"publisher"}]},{"award":["226602\/Z\/22\/Z"],"award-info":[{"award-number":["226602\/Z\/22\/Z"]}],"id":[{"id":"https:\/\/ror.org\/029chgv08","id-type":"ROR","asserted-by":"publisher"}]},{"award":["306920\/Z\/23\/Z"],"award-info":[{"award-number":["306920\/Z\/23\/Z"]}],"id":[{"id":"https:\/\/ror.org\/029chgv08","id-type":"ROR","asserted-by":"publisher"}]},{"award":["319534\/Z\/24\/Z"],"award-info":[{"award-number":["319534\/Z\/24\/Z"]}],"id":[{"id":"https:\/\/ror.org\/029chgv08","id-type":"ROR","asserted-by":"publisher"}]},{"award":["NIHR200915"],"award-info":[{"award-number":["NIHR200915"]}],"id":[{"id":"https:\/\/ror.org\/0187kwz08","id-type":"ROR","asserted-by":"publisher"}]},{"name":"National Health and Medical Research Council Australia","award":["2034741"],"award-info":[{"award-number":["2034741"]}]},{"name":"SciLife Lab and Wallenberg Data Driven Life Science Program","award":["KAW 2020.0239"],"award-info":[{"award-number":["KAW 2020.0239"]}]},{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"crossref","award":["BB\/CCG1860\/1"],"award-info":[{"award-number":["BB\/CCG1860\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]},{"award":["U19AI174998"],"award-info":[{"award-number":["U19AI174998"]}],"id":[{"id":"https:\/\/ror.org\/001d55x84","id-type":"ROR","asserted-by":"publisher"}]},{"award":["1R01AI185544-01A1"],"award-info":[{"award-number":["1R01AI185544-01A1"]}],"id":[{"id":"https:\/\/ror.org\/001d55x84","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014013","name":"UKRI","doi-asserted-by":"crossref","award":["UKRI2317"],"award-info":[{"award-number":["UKRI2317"]}],"id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"crossref"}]},{"award":["PLEIADES 101219784"],"award-info":[{"award-number":["PLEIADES 101219784"]}],"id":[{"id":"https:\/\/ror.org\/0472cxd90","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Public microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not uniformly assembled, quality controlled, annotated or searchable at scale. Here we present AllTheBacteria, an open, community-built resource that transforms public bacterial short-read whole-genome sequencing reads into a uniformly processed discovery platform. The current analysed release contains 2,440,377 high-quality bacterial and archaeal genomes from 11,273 species, together with standardized taxonomic assignments, genome annotations, antimicrobial resistance calls, antiphage-defence annotations, protein structure predictions and AI-ready sequence tables. We show that this infrastructure enables applications that would otherwise be impractical, from global sequence search and outbreak contextualization to pangenome method development, antimicrobial resistance reservoir mapping and antiphage-defence ecology. As a stringent experimental demonstration, we mined 3,919,096 encrypted peptide fragments from AllTheBacteria proteomes using our deep learning model APEX 1.1, identifying 1,867 candidates with predicted antimicrobial activity. We synthesized 24 representative peptides and tested them against 20 clinically relevant bacterial strains, including antibiotic-resistant pathogens. Multiple peptides showed low-micromolar activity, membrane-responsive conformational transitions and selective envelope perturbation. A lead molecule, ATB20, reduced\n                  <jats:italic>Acinetobacter baumannii<\/jats:italic>\n                  burden in a murine skin abscess model with efficacy comparable to polymyxin B and no overt toxicity. Together, these results establish AllTheBacteria as both a foundational community resource for microbiology and a renewable engine for AI-guided antimicrobial discovery.\n                <\/jats:p>","DOI":"10.1101\/2024.03.08.584059","type":"posted-content","created":{"date-parts":[[2024,3,11]],"date-time":"2024-03-11T09:40:11Z","timestamp":1710150011000},"source":"Crossref","is-referenced-by-count":98,"title":["AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8060-4335","authenticated-orcid":false,"given":"Martin","family":"Hunt","sequence":"first","affiliation":[{"name":"Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK"},{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK"},{"name":"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom"},{"name":"National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, United Kingdom"},{"name":"Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcelo D. T.","family":"Torres","sequence":"additional","affiliation":[{"name":"Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania 19104, USA"},{"name":"Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania; Philadelphia, Pennsylvania 19104, USA"},{"name":"Penn Institute for Computational Science, University of Pennsylvania; Philadelphia, Pennsylvania 19104, USA"},{"name":"Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1243-0767","authenticated-orcid":false,"given":"Nabil-Fareed","family":"Alikhan","sequence":"additional","affiliation":[{"name":"Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK"},{"name":"Centre for Genomic Pathogen Surveillance, Pandemic Sciences Institute, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4422-9520","authenticated-orcid":false,"given":"Daniel","family":"Anderson","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1308-865X","authenticated-orcid":false,"given":"Maria Luiza","family":"Andreani","sequence":"additional","affiliation":[{"name":"Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-9910-7374","authenticated-orcid":false,"given":"Josefin","family":"Blom","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, SciLifeLab, Ume\u00e5 University, Ume\u00e5, Sweden"},{"name":"Laboratory for Molecular Infection Medicine Sweden (MIMS), Ume\u00e5 University, Ume\u00e5, Sweden"},{"name":"Ume\u00e5 Centre for Microbial Research (UCMR), Ume\u00e5 University, Ume\u00e5, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5885-4186","authenticated-orcid":false,"given":"George","family":"Bouras","sequence":"additional","affiliation":[{"name":"School of Medicine, College of Health, Adelaide University, Adelaide, Australia"},{"name":"The Department of Surgery \u2013 Otolaryngology Head and Neck Surgery, The Basil Hetzel Institute for Translational Research, Woodville South, South Australia 5011, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0584-4099","authenticated-orcid":false,"given":"Fiona S.L.","family":"Brinkman","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3677-0192","authenticated-orcid":false,"given":"Laura M.","family":"Carroll","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, SciLifeLab, Ume\u00e5 University, Ume\u00e5, Sweden"},{"name":"Laboratory for Molecular Infection Medicine Sweden (MIMS), Ume\u00e5 University, Ume\u00e5, Sweden"},{"name":"Ume\u00e5 Centre for Microbial Research (UCMR), Ume\u00e5 University, Ume\u00e5, Sweden"},{"name":"Integrated Science Lab (IceLab), Ume\u00e5 University, Ume\u00e5, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9564-7952","authenticated-orcid":false,"given":"Matthew A.","family":"Croxen","sequence":"additional","affiliation":[{"name":"Women and Children\u2019s Health Research Institute, University of Alberta, Edmonton, Alberta, Canada"},{"name":"Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2188-5659","authenticated-orcid":false,"given":"R. Andres","family":"Floto","sequence":"additional","affiliation":[{"name":"Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK"},{"name":"Victor Phillip Dahdaleh Heart Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3683-6208","authenticated-orcid":false,"given":"Michael B.","family":"Hall","sequence":"additional","affiliation":[{"name":"Frazer Institute, The University of Queensland, Herston, QLD 4029, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane","family":"Hawkey","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, School of Translational Medicine, Monash University, Melbourne, Victoria, Australia"},{"name":"Centre to Impact AMR, Monash University, Melbourne, Victoria, Australia"},{"name":"Department of Microbiology, Monash University, Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3859-4073","authenticated-orcid":false,"given":"Samuel T.","family":"Horsfield","sequence":"additional","affiliation":[{"name":"Institute of Biology, University of Neuch\u00e2tel, Rue \u00c9mile-Argand 11, 2000 Neuch\u00e2tel, Switzerland"},{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4735-4709","authenticated-orcid":false,"given":"Baofeng","family":"Jia","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jake A","family":"Lacey","sequence":"additional","affiliation":[{"name":"Microbiological Diagnostics Unit Public Health Laboratory, University of Melbourne, Victoria, Australia"},{"name":"Department of Microbiology and Immunology, Peter Doherty Institure at the University of Melbourne, Victoria, Australia"},{"name":"Centre for Pathogen Genomics, University of Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyun-Su","family":"Lee","sequence":"additional","affiliation":[{"name":"Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania 19104, USA"},{"name":"Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania; Philadelphia, Pennsylvania 19104, USA"},{"name":"Penn Institute for Computational Science, University of Pennsylvania; Philadelphia, Pennsylvania 19104, USA"},{"name":"Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leandro","family":"Lima","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neil","family":"MacAlasdair","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8899-3323","authenticated-orcid":false,"given":"Sudaraka","family":"Mallawaarachchi","sequence":"additional","affiliation":[{"name":"Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia"},{"name":"Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Department of Biostatistics, University of Oslo, Oslo, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5608-0423","authenticated-orcid":false,"given":"William","family":"Matlock","sequence":"additional","affiliation":[{"name":"Centre for Evolution, University of Bath, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9949-6936","authenticated-orcid":false,"given":"Ahmed M.","family":"Moustafa","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Hepatology, and Nutrition, Children\u2019s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA"},{"name":"Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA"},{"name":"Center for Microbial Medicine, Children\u2019s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA"},{"name":"Department of Biomedical and Health Informatics, Children\u2019s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"III","given":"Robert","family":"Petit","sequence":"additional","affiliation":[{"name":"Dept Bison Wrangling, Cowboy University, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8315-5343","authenticated-orcid":false,"given":"Vignesh","family":"Ramnath","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, SciLifeLab, Ume\u00e5 University, Ume\u00e5, Sweden"},{"name":"Laboratory for Molecular Infection Medicine Sweden (MIMS), Ume\u00e5 University, Ume\u00e5, Sweden"},{"name":"Ume\u00e5 Centre for Microbial Research (UCMR), Ume\u00e5 University, Ume\u00e5, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7435-6435","authenticated-orcid":false,"given":"Vishnu","family":"Raghuram","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology, SciLifeLab, Ume\u00e5 University, Ume\u00e5, Sweden"},{"name":"Laboratory for Molecular Infection Medicine Sweden (MIMS), Ume\u00e5 University, Ume\u00e5, Sweden"},{"name":"Ume\u00e5 Centre for Microbial Research (UCMR), Ume\u00e5 University, Ume\u00e5, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1976-4153","authenticated-orcid":false,"given":"Matthew J.","family":"Russell","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Theo","family":"Sanderson","sequence":"additional","affiliation":[{"name":"London School of Hygiene and Tropical Medicine, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-2399-4156","authenticated-orcid":false,"given":"Timo","family":"Saratto","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4216-2721","authenticated-orcid":false,"given":"Oliver","family":"Schwengers","sequence":"additional","affiliation":[{"name":"Bioinformatics and Systems Biology, Justus Liebig University Giessen, Ludwigsplatz 13-15, 35390 Giessen, Hesse, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6046-610X","authenticated-orcid":false,"given":"Torsten","family":"Seemann","sequence":"additional","affiliation":[{"name":"Microbiological Diagnostics Unit Public Health Laboratory, University of Melbourne, Victoria, Australia"},{"name":"Department of Microbiology and Immunology, Peter Doherty Institure at the University of Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liam P.","family":"Shaw","sequence":"additional","affiliation":[{"name":"School of Biochemistry and Biomedical Sciences, University of Bristol, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8099-8258","authenticated-orcid":false,"given":"Wei","family":"Shen","sequence":"additional","affiliation":[{"name":"Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas","family":"Thomson","sequence":"additional","affiliation":[{"name":"Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4397-2224","authenticated-orcid":false,"given":"Gerry","family":"Tonkin-Hill","sequence":"additional","affiliation":[{"name":"Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia"},{"name":"Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3305-2320","authenticated-orcid":false,"given":"Jackie","family":"Toussaint","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK"},{"name":"School of the Biological Sciences, University of Cambridge, Cambridge, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2106-8130","authenticated-orcid":false,"given":"Thanh Le","family":"Viet","sequence":"additional","affiliation":[{"name":"Theiagen Genomics, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johanna von","family":"Wachsmann","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fangping","family":"Wan","sequence":"additional","affiliation":[{"name":"Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania 19104, USA"},{"name":"Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania; Philadelphia, Pennsylvania 19104, USA"},{"name":"Penn Institute for Computational Science, University of Pennsylvania; Philadelphia, Pennsylvania 19104, USA"},{"name":"Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4597-2471","authenticated-orcid":false,"given":"Aaron","family":"Weimann","sequence":"additional","affiliation":[{"name":"Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK"},{"name":"Victor Phillip Dahdaleh Heart Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1212-2286","authenticated-orcid":false,"given":"Rachel M.","family":"Wheatley","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Queen\u2019s University Belfast, Belfast, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maciej","family":"Wiatrak","sequence":"additional","affiliation":[{"name":"Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK"},{"name":"Victor Phillip Dahdaleh Heart Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5032-1932","authenticated-orcid":false,"given":"Ouli","family":"Xie","sequence":"additional","affiliation":[{"name":"Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK"},{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cesar de la","family":"Fuente-Nunez","sequence":"additional","affiliation":[{"name":"Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania 19104, USA"},{"name":"Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania; Philadelphia, Pennsylvania 19104, USA"},{"name":"Penn Institute for Computational Science, University of Pennsylvania; Philadelphia, Pennsylvania 19104, USA"},{"name":"Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5360-1254","authenticated-orcid":false,"given":"John A.","family":"Lees","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8466-7547","authenticated-orcid":false,"given":"Zamin","family":"Iqbal","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK"},{"name":"Centre for Evolution, University of Bath, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026070910453978000_2024.03.08.584059v8.1","doi-asserted-by":"publisher","DOI":"10.1038\/nature19057"},{"key":"2026070910453978000_2024.03.08.584059v8.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2308-7"},{"key":"2026070910453978000_2024.03.08.584059v8.3","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2267-z"},{"key":"2026070910453978000_2024.03.08.584059v8.4","first-page":"000818","article-title":"Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks","volume":"8","year":"2022","journal-title":"Microb. Genomics"},{"key":"2026070910453978000_2024.03.08.584059v8.5","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf1208"},{"key":"2026070910453978000_2024.03.08.584059v8.6","doi-asserted-by":"publisher","DOI":"10.1101\/2024.07.30.605881"},{"key":"2026070910453978000_2024.03.08.584059v8.7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3001421"},{"key":"2026070910453978000_2024.03.08.584059v8.8","doi-asserted-by":"crossref","first-page":"D743","DOI":"10.1093\/nar\/gkaf1040","article-title":"GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes","volume":"54","year":"2026","journal-title":"Nucleic Acids Res"},{"key":"2026070910453978000_2024.03.08.584059v8.9","doi-asserted-by":"crossref","first-page":"6360","DOI":"10.1038\/s41467-025-61152-y","article-title":"Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria","volume":"16","year":"2025","journal-title":"Nat. Commun"},{"key":"2026070910453978000_2024.03.08.584059v8.10","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-66413-4"},{"key":"2026070910453978000_2024.03.08.584059v8.11","doi-asserted-by":"publisher","DOI":"10.64898\/2026.03.04.26347163"},{"key":"2026070910453978000_2024.03.08.584059v8.12","first-page":"e01708","article-title":"Putative azithromycin resistance mutations in Chlamydia trachomatis are globally distributed but arose before azithromycin was discovered","volume":"70","year":"2026","journal-title":"Antimicrob. Agents Chemother"},{"key":"2026070910453978000_2024.03.08.584059v8.13","doi-asserted-by":"crossref","unstructured":"McCartney, A. L. & Hoyles, L . Host interactions of bioactive molecules produced by Klebsiella spp. Microbiota Host 3, (2025).","DOI":"10.1530\/MAH-24-0011"},{"key":"2026070910453978000_2024.03.08.584059v8.14","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf606"},{"key":"2026070910453978000_2024.03.08.584059v8.15","doi-asserted-by":"crossref","first-page":"e2523357123","DOI":"10.1073\/pnas.2523357123","article-title":"Imported, not invented, genes prevail among Escherichia coli ORFans","volume":"123","year":"2026","journal-title":"Proc. Natl. Acad. Sci"},{"key":"2026070910453978000_2024.03.08.584059v8.16","doi-asserted-by":"publisher","DOI":"10.64898\/2026.01.05.697752"},{"key":"2026070910453978000_2024.03.08.584059v8.17","doi-asserted-by":"publisher","DOI":"10.64898\/2026.02.04.703695"},{"key":"2026070910453978000_2024.03.08.584059v8.18","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1038\/s41592-025-02625-2","article-title":"Efficient and robust search of microbial genomes via phylogenetic compression","volume":"22","year":"2025","journal-title":"Nat. Methods"},{"key":"2026070910453978000_2024.03.08.584059v8.19","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-025-02812-8"},{"key":"2026070910453978000_2024.03.08.584059v8.20","doi-asserted-by":"publisher","DOI":"10.64898\/2025.12.30.695181"},{"key":"2026070910453978000_2024.03.08.584059v8.21","doi-asserted-by":"crossref","first-page":"100637","DOI":"10.1016\/j.clinpr.2026.100637","article-title":"The 2026 meningococcal serogroup B cluster in the United Kingdom: a case for strategic reform","volume":"30","year":"2026","journal-title":"Clin. Infect. Pract"},{"key":"2026070910453978000_2024.03.08.584059v8.22","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.s547"},{"key":"2026070910453978000_2024.03.08.584059v8.23","doi-asserted-by":"publisher","DOI":"10.64898\/2026.01.21.700884"},{"key":"2026070910453978000_2024.03.08.584059v8.24","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.2602.17201"},{"key":"2026070910453978000_2024.03.08.584059v8.25","doi-asserted-by":"crossref","unstructured":"Li, H . BWT construction and search at the terabase scale. Bioinformatics 20, (2024).","DOI":"10.1093\/bioinformatics\/btae717"},{"key":"2026070910453978000_2024.03.08.584059v8.26","doi-asserted-by":"publisher","DOI":"10.64898\/2026.05.24.727514"},{"key":"2026070910453978000_2024.03.08.584059v8.27","doi-asserted-by":"publisher","DOI":"10.1038\/S41586-021-03819-2"},{"key":"2026070910453978000_2024.03.08.584059v8.28","doi-asserted-by":"publisher","DOI":"10.64898\/2026.04.28.721069"},{"key":"2026070910453978000_2024.03.08.584059v8.29","doi-asserted-by":"publisher","DOI":"10.1101\/2025.07.20.665723"},{"key":"2026070910453978000_2024.03.08.584059v8.30","doi-asserted-by":"publisher","DOI":"10.1038\/nature10388"},{"key":"2026070910453978000_2024.03.08.584059v8.31","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad943"},{"key":"2026070910453978000_2024.03.08.584059v8.32","doi-asserted-by":"publisher","DOI":"10.1007\/s00438-004-1048-y"},{"key":"2026070910453978000_2024.03.08.584059v8.33","doi-asserted-by":"publisher","DOI":"10.1128\/jb.178.7.2044-2050.1996"},{"key":"2026070910453978000_2024.03.08.584059v8.34","doi-asserted-by":"publisher","DOI":"10.1186\/s12862-017-0942-y"},{"key":"2026070910453978000_2024.03.08.584059v8.35","first-page":"000522","article-title":"Phylogeny of Salmonella enterica subspecies arizonae by whole-genome sequencing reveals high incidence of polyphyly and low phase 1 H antigen variability","volume":"7","year":"2021","journal-title":"Microb. Genomics"},{"key":"2026070910453978000_2024.03.08.584059v8.36","doi-asserted-by":"publisher","DOI":"10.64898\/2025.12.24.696407"},{"key":"2026070910453978000_2024.03.08.584059v8.37","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2024.01.015"},{"key":"2026070910453978000_2024.03.08.584059v8.38","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1016\/j.tibtech.2024.09.008","article-title":"Peptides from non-immune proteins target infections through antimicrobial and immunomodulatory properties","volume":"43","year":"2025","journal-title":"Trends Biotechnol"},{"key":"2026070910453978000_2024.03.08.584059v8.39","doi-asserted-by":"crossref","first-page":"2153","DOI":"10.1038\/s41564-025-02061-0","article-title":"Deep learning reveals antibiotics in the archaeal proteome","volume":"10","year":"2025","journal-title":"Nat. Microbiol"},{"key":"2026070910453978000_2024.03.08.584059v8.40","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac345"},{"key":"2026070910453978000_2024.03.08.584059v8.41","first-page":"67","article-title":"Mining for encrypted peptide antibiotics in the human proteome","volume":"6","year":"2022","journal-title":"Nat. Biomed. Eng"},{"key":"2026070910453978000_2024.03.08.584059v8.42","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2024.07.027"},{"key":"2026070910453978000_2024.03.08.584059v8.43","doi-asserted-by":"publisher","DOI":"10.1016\/J.CELL.2024.05.013"},{"key":"2026070910453978000_2024.03.08.584059v8.44","doi-asserted-by":"publisher","DOI":"10.1101\/2025.11.12.688105"},{"key":"2026070910453978000_2024.03.08.584059v8.45","doi-asserted-by":"crossref","unstructured":"Jesudason, T . EMBL\u2013EBI\u2019s AMR portal: a new gateway in global antimicrobial resistance research. Lancet Microbe 7, (2026).","DOI":"10.1016\/j.lanmic.2025.101326"},{"key":"2026070910453978000_2024.03.08.584059v8.46","doi-asserted-by":"publisher","DOI":"10.1126\/science.ade2574"},{"key":"2026070910453978000_2024.03.08.584059v8.47","doi-asserted-by":"crossref","unstructured":"Bartlett, A. , Padfield, D. , Lear, L. , Bendall, R. & Vos, M . A comprehensive list of bacterial pathogens infecting humans. Microbiology 168, (2022).","DOI":"10.1099\/mic.0.001269"},{"key":"2026070910453978000_2024.03.08.584059v8.48","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"2026070910453978000_2024.03.08.584059v8.49","doi-asserted-by":"publisher","DOI":"10.1101\/2023.11.20.567879"},{"key":"2026070910453978000_2024.03.08.584059v8.50","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgg.2021.03.006"},{"key":"2026070910453978000_2024.03.08.584059v8.51","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005944"},{"key":"2026070910453978000_2024.03.08.584059v8.52","doi-asserted-by":"publisher","DOI":"10.1126\/science.abj6987"},{"key":"2026070910453978000_2024.03.08.584059v8.53","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06457-y"},{"key":"2026070910453978000_2024.03.08.584059v8.54","doi-asserted-by":"publisher","DOI":"10.1034\/j.1399-0039.2000.550314.x"},{"key":"2026070910453978000_2024.03.08.584059v8.55","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac1011"},{"key":"2026070910453978000_2024.03.08.584059v8.56","doi-asserted-by":"publisher","DOI":"10.1111\/tan.15549"},{"key":"2026070910453978000_2024.03.08.584059v8.57","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-01940-w"},{"key":"2026070910453978000_2024.03.08.584059v8.58","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2021.0237"},{"key":"2026070910453978000_2024.03.08.584059v8.59","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-91456-0"},{"key":"2026070910453978000_2024.03.08.584059v8.60","doi-asserted-by":"crossref","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications","volume":"3","year":"2018","journal-title":"Wellcome Open Res"},{"key":"2026070910453978000_2024.03.08.584059v8.61","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki177"},{"key":"2026070910453978000_2024.03.08.584059v8.62","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae968"},{"key":"2026070910453978000_2024.03.08.584059v8.63","doi-asserted-by":"publisher","DOI":"10.1101\/2021.05.03.442509"},{"key":"2026070910453978000_2024.03.08.584059v8.64","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3820"},{"key":"2026070910453978000_2024.03.08.584059v8.65","first-page":"e000339","article-title":"Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive","volume":"6","year":"2020","journal-title":"Microb. Genomics"},{"key":"2026070910453978000_2024.03.08.584059v8.66","first-page":"001428","article-title":"Fast and accurate in silico antigen typing with Kaptive 3","volume":"11","year":"2025","journal-title":"Microb. Genomics"},{"key":"2026070910453978000_2024.03.08.584059v8.67","first-page":"mgen000878","article-title":"An update to the database for Acinetobacter baumannii capsular polysaccharide locus typing extends the extensive and diverse repertoire of genes found at and outside the K locus","volume":"8","year":"2022","journal-title":"Microb. Genomics"},{"key":"2026070910453978000_2024.03.08.584059v8.68","first-page":"000728","article-title":"ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data","volume":"7","year":"2021","journal-title":"Microb. Genomics"},{"key":"2026070910453978000_2024.03.08.584059v8.69","first-page":"000704","article-title":"Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping","volume":"7","year":"2021","journal-title":"Microb. Genomics"},{"key":"2026070910453978000_2024.03.08.584059v8.70","first-page":"e00190","article-title":"E. hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus","volume":"57","year":"2019","journal-title":"J. Clin. Microbiol"},{"key":"2026070910453978000_2024.03.08.584059v8.71","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-24448-3"},{"key":"2026070910453978000_2024.03.08.584059v8.72","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.42.8.3819-3822.2004"},{"key":"2026070910453978000_2024.03.08.584059v8.73","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-019-0650-x"},{"key":"2026070910453978000_2024.03.08.584059v8.74","first-page":"001189","article-title":"pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections","volume":"10","year":"2024","journal-title":"Microb. Genomics"},{"key":"2026070910453978000_2024.03.08.584059v8.75","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.42.1.320-328.2004"},{"key":"2026070910453978000_2024.03.08.584059v8.76","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6976.2006.00057.x"},{"key":"2026070910453978000_2024.03.08.584059v8.77","doi-asserted-by":"publisher","DOI":"10.1016\/j.vaccine.2016.08.015"},{"key":"2026070910453978000_2024.03.08.584059v8.78","first-page":"e02161","article-title":"Meningococcal Deduced Vaccine Antigen Reactivity (MenDeVAR) Index: a Rapid and Accessible Tool That Exploits Genomic Data in Public Health and Clinical Microbiology Applications","volume":"59","year":"2020","journal-title":"J. Clin. Microbiol"},{"key":"2026070910453978000_2024.03.08.584059v8.79","first-page":"000688","article-title":"GBS-SBG - GBS Serotyping by Genome Sequencing","volume":"7","year":"2021","journal-title":"Microb. Genomics"},{"key":"2026070910453978000_2024.03.08.584059v8.80","first-page":"mgen000904","article-title":"PneumoKITy: A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data","volume":"8","year":"2022","journal-title":"Microb. Genomics"},{"key":"2026070910453978000_2024.03.08.584059v8.81","first-page":"mgen001007","article-title":"Development of Kaptive databases for Vibrio parahaemolyticus O- and K-antigen genotyping","volume":"9","year":"2023","journal-title":"Microb. Genomics"},{"key":"2026070910453978000_2024.03.08.584059v8.82","doi-asserted-by":"crossref","unstructured":"Carroll, L. M. , Cheng, R. A. & Kovac, J . No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods. Front. Microbiol. 11, (2020).","DOI":"10.3389\/fmicb.2020.580691"},{"key":"2026070910453978000_2024.03.08.584059v8.83","doi-asserted-by":"crossref","unstructured":"Schwengers, O. et al. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb. Genomics 7, (2021).","DOI":"10.1099\/mgen.0.000685"},{"key":"2026070910453978000_2024.03.08.584059v8.84","doi-asserted-by":"publisher","DOI":"10.1038\/S41592-022-01488-1"},{"key":"2026070910453978000_2024.03.08.584059v8.85","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3988"},{"key":"2026070910453978000_2024.03.08.584059v8.86","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl582"},{"key":"2026070910453978000_2024.03.08.584059v8.87","doi-asserted-by":"publisher","DOI":"10.1093\/NAR\/GKAA991"},{"key":"2026070910453978000_2024.03.08.584059v8.88","doi-asserted-by":"publisher","DOI":"10.1038\/299371a0"},{"key":"2026070910453978000_2024.03.08.584059v8.89","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1016\/bs.mie.2021.11.003","volume-title":"Antimicrobial Peptides","volume":"663","year":"2022"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2024.03.08.584059","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T17:45:53Z","timestamp":1783619153000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2024.03.08.584059"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,11]]},"references-count":89,"URL":"https:\/\/doi.org\/10.1101\/2024.03.08.584059","relation":{},"subject":[],"published":{"date-parts":[[2024,3,11]]},"subtype":"preprint"}}