{"doi":"10.1101/2024.03.08.584059","title":"AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics","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>","journal":null,"year":null,"id":656342,"datarank":0.6698862177981877,"base_score":4.465908118654584,"endowment":4.465908118654584,"self_citation_contribution":0.6698862177981877,"citation_network_contribution":0.0,"self_endowment_contribution":0.6698862177981877,"citer_contribution":0.0,"corpus_percentile":70.8,"corpus_rank":3995,"citation_count":86,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":428219,"name":"Marcelo D. T. Torres","orcid":"0000-0002-6165-9138","position":1,"is_corresponding":false},{"id":867292,"name":"Nabil-Fareed Alikhan","orcid":"0000-0002-1243-0767","position":2,"is_corresponding":false},{"id":1325655,"name":"D.P. Anderson","orcid":"0000-0003-4422-9520","position":3,"is_corresponding":false},{"id":1713322,"name":"Maria Luiza Andreani","orcid":"0000-0002-1308-865X","position":4,"is_corresponding":false},{"id":1481842,"name":"J. Blom","orcid":"0009-0000-9910-7374","position":5,"is_corresponding":false},{"id":881962,"name":"George Bouras","orcid":"0000-0002-5885-4186","position":6,"is_corresponding":false},{"id":1287747,"name":"Fiona S. L. Brinkman","orcid":"0000-0002-0584-4099","position":7,"is_corresponding":false},{"id":829286,"name":"Laura M. Carroll","orcid":"0000-0002-3677-0192","position":8,"is_corresponding":false},{"id":1287741,"name":"Matthew A. Croxen","orcid":"0000-0002-9564-7952","position":9,"is_corresponding":false},{"id":503205,"name":"R. Andrés Floto","orcid":"0000-0002-2188-5659","position":10,"is_corresponding":false},{"id":1468870,"name":"Michael B. Hall","orcid":"0000-0003-3683-6208","position":11,"is_corresponding":false},{"id":312482,"name":"Jane Hawkey","orcid":"0000-0001-9661-5293","position":12,"is_corresponding":false},{"id":1713323,"name":"Samuel T. Horsfield","orcid":"0000-0002-3859-4073","position":13,"is_corresponding":false},{"id":1287726,"name":"Baofeng Jia","orcid":"0000-0002-4735-4709","position":14,"is_corresponding":false},{"id":1713324,"name":"Jake A Lacey","orcid":null,"position":15,"is_corresponding":false},{"id":1713325,"name":"Hyun-Su Lee","orcid":null,"position":16,"is_corresponding":false},{"id":1161207,"name":"Leandro Lima","orcid":"0000-0001-8976-2762","position":17,"is_corresponding":false},{"id":1713326,"name":"Neil MacAlasdair","orcid":null,"position":18,"is_corresponding":false},{"id":1713327,"name":"Sudaraka Mallawaarachchi","orcid":"0000-0001-8899-3323","position":19,"is_corresponding":false},{"id":1580364,"name":"William Matlock","orcid":"0000-0001-5608-0423","position":20,"is_corresponding":false},{"id":394505,"name":"Ahmed M. Moustafa","orcid":"0000-0002-9949-6936","position":21,"is_corresponding":false},{"id":1713328,"name":"Robert Petit","orcid":null,"position":22,"is_corresponding":false},{"id":1713329,"name":"Vignesh Ramnath","orcid":"0009-0005-8315-5343","position":23,"is_corresponding":false},{"id":311515,"name":"Vishnu Raghuram","orcid":"0000-0002-7435-6435","position":24,"is_corresponding":false},{"id":1713330,"name":"Matthew J. Russell","orcid":"0000-0002-1976-4153","position":25,"is_corresponding":false},{"id":472005,"name":"Theo Sanderson","orcid":"0000-0003-4177-2851","position":26,"is_corresponding":false},{"id":1713332,"name":"Timo Saratto","orcid":"0009-0004-2399-4156","position":27,"is_corresponding":false},{"id":1526000,"name":"Oliver Schwengers","orcid":"0000-0003-4216-2721","position":28,"is_corresponding":false},{"id":80555,"name":"Torsten Seemann","orcid":"0000-0001-6046-610X","position":29,"is_corresponding":false},{"id":305630,"name":"Liam P. Shaw","orcid":"0000-0001-7332-0820","position":30,"is_corresponding":false},{"id":246136,"name":"Wei Shen","orcid":"0000-0002-8099-8258","position":31,"is_corresponding":false},{"id":94725,"name":"Nicholas Thomson","orcid":null,"position":32,"is_corresponding":false},{"id":576985,"name":"Gerry Tonkin‐Hill","orcid":"0000-0003-4397-2224","position":33,"is_corresponding":false},{"id":1713335,"name":"Jackie Toussaint","orcid":"0000-0002-3305-2320","position":34,"is_corresponding":false},{"id":705218,"name":"Thanh Le-Viet","orcid":"0000-0002-2106-8130","position":35,"is_corresponding":false},{"id":1713336,"name":"Johanna von Wachsmann","orcid":null,"position":36,"is_corresponding":false},{"id":1713337,"name":"Fangping Wan","orcid":null,"position":37,"is_corresponding":false},{"id":989133,"name":"Aaron Weimann","orcid":"0000-0003-4597-2471","position":38,"is_corresponding":false},{"id":1713338,"name":"Rachel M. Wheatley","orcid":"0000-0003-1212-2286","position":39,"is_corresponding":false},{"id":1713339,"name":"Maciej Wiatrak","orcid":null,"position":40,"is_corresponding":false},{"id":1563742,"name":"Ouli Xie","orcid":"0000-0002-5032-1932","position":41,"is_corresponding":false},{"id":1713340,"name":"Cesar de la Fuente-Nunez","orcid":null,"position":42,"is_corresponding":false},{"id":392157,"name":"John A. Lees","orcid":"0000-0001-5360-1254","position":43,"is_corresponding":false},{"id":555725,"name":"Zamin Iqbal","orcid":"0000-0001-8466-7547","position":44,"is_corresponding":false},{"id":944961,"name":"Martin Hunt","orcid":"0000-0002-8060-4335","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics","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>","is_dataset_classified":null,"base_score":4.406719247264253,"endowment":4.406719247264253,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"42465405","pmcid":null,"openalex_id":"https://openalex.org/W4392644277","authors":[],"funders":[{"funder_name":"","grant_id":"220540/Z/20/A","title":null},{"funder_name":"","grant_id":"226602/Z/22/Z","title":null},{"funder_name":"","grant_id":"306920/Z/23/Z","title":null},{"funder_name":"","grant_id":"319534/Z/24/Z","title":null},{"funder_name":"","grant_id":"NIHR200915","title":null},{"funder_name":"National Health and Medical Research Council Australia","grant_id":"2034741","title":null},{"funder_name":"SciLife Lab and Wallenberg Data Driven Life Science Program","grant_id":"KAW 2020.0239","title":null},{"funder_name":"BBSRC","grant_id":"BB/CCG1860/1","title":null},{"funder_name":"","grant_id":"U19AI174998","title":null},{"funder_name":"","grant_id":"1R01AI185544-01A1","title":null},{"funder_name":"UKRI","grant_id":"UKRI2317","title":null},{"funder_name":"","grant_id":"PLEIADES 101219784","title":null}],"total_grants":12,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[{"year":2024,"count":14},{"year":2025,"count":40},{"year":2026,"count":27}],"oa_status":"green","license":"cc-by","oa_locations":[{"url":"https://www.biorxiv.org/content/biorxiv/early/2024/03/11/2024.03.08.584059.full.pdf","host_type":"repository"},{"url":"https://www.biorxiv.org/content/biorxiv/early/2024/03/11/2024.03.08.584059.full.pdf","host_type":"repository"},{"url":"https://syndication.highwire.org/content/doi/10.1101/2024.03.08.584059","host_type":"publisher"},{"url":"https://doi.org/10.1101/2024.03.08.584059","host_type":"repository"},{"url":"https://pubmed.ncbi.nlm.nih.gov/42465405","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13370402/","host_type":"repository"},{"url":"https://pure.qub.ac.uk/en/publications/32bc0d57-64c2-448e-8836-2d4f9bc62643","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13370402/pdf/nihpp-2024.03.08.584059v8.pdf","host_type":"repository"},{"url":"https://pureadmin.qub.ac.uk/ws/files/697655094/AllTheBacteria_a_community_resource_empowers_biology_and_discovers_novel_peptide_antibiotics.pdf","host_type":"repository"}],"fields_of_study":["Genomics and Phylogenetic Studies","Microbial Community Ecology and Physiology","Microbial Metabolic Engineering and Bioproduction"],"mesh_terms":[],"keywords":["Bacterial genome size","Genome","Computational biology","Computer science","Biology","World Wide Web","Genetics","Gene"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-11T20:33:21.183174Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}