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Here, we present VirulentHunter, a novel deep learning framework that enable simultaneous VF identification and classification directly from protein sequences by leveraging the crucial step of fine-tuning pretrained protein language model. We curate a comprehensive VF database by integrating diverse public resources and expanding VF category annotations. Our benchmarking results demonstrate that VirulentHunter outperforms existing methods, particularly in identifying VFs lacking detectable homologs. Additionally, strain-level analysis using VirulentHunter highlights distinct pathogenicity profiles between Mycobacterium tuberculosis and Mycobacterium avium, revealing enrichment in VFs related to adherence, effector delivery systems, and immune modulation in M. tuberculosis, compared to biofilm formation and motility in M. avium. Furthermore, metagenomic profiling of gut microbiota from inflammatory bowel disease patient reveals a depletion of VFs associated with immune homeostasis. These results underscore the versatility of VirulentHunter as a powerful tool for VF analysis across diverse applications. To facilitate broader accessibility, we provide a freely accessible web service for VF prediction (http:\/\/www.unimd.org\/VirulentHunter), accommodating protein sequences, genomes, and metagenomic data.<\/jats:p>","DOI":"10.1093\/bib\/bbaf271","type":"journal-article","created":{"date-parts":[[2025,6,16]],"date-time":"2025-06-16T07:11:22Z","timestamp":1750057882000},"source":"Crossref","is-referenced-by-count":10,"title":["VirulentHunter: deep learning-based virulence factor predictor illuminates pathogenicity in diverse microbial contexts"],"prefix":"10.1093","volume":"26","author":[{"given":"Chen","family":"Chen","sequence":"first","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University , Dongchuan Road 500, Shanghai 200241 ,","place":["China"]},{"name":"School of Mathematics and Computer Science, Ningxia Normal University , College Road, Guyuan City, Ningxia 756099 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0240-5736","authenticated-orcid":false,"given":"Yong","family":"Xu","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University , Dongchuan Road 500, Shanghai 200241 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7851-7064","authenticated-orcid":false,"given":"Jian","family":"Ouyang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University , Dongchuan Road 500, Shanghai 200241 ,","place":["China"]},{"name":"Henan International Joint Laboratory of Infection and Immunity, Henan Key Laboratory of Critical Care Medicine, Department of Emergency Medicine, The First Affiliated Hospital, Zhengzhou University , East Jianshe Road No. 1, Zhengzhou 450052 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangyi","family":"Xiong","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University , Dongchuan Road 500, Shanghai 200241 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pawe\u0142 P","family":"\u0141abaj","sequence":"additional","affiliation":[{"name":"Ma\u0142opolska Centre of Biotechnology, Jagiellonian University , Gronostajowa 7A, 30-387 Krak\u00f3w ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agnieszka","family":"Chmielarczyk","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Department of Microbiology, Jagiellonian University , ul. Czysta 18, 31-121 ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"R\u00f3\u017ca\u0144ska","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Department of Microbiology, Jagiellonian University , ul. Czysta 18, 31-121 ,","place":["Poland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University , Dongchuan Road 500, Shanghai 200241 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keyang","family":"Liu","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University , Dongchuan Road 500, Shanghai 200241 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tieliu","family":"Shi","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University , Dongchuan Road 500, Shanghai 200241 ,","place":["China"]},{"name":"Key Laboratory of Advanced Theory and Application in Statistics and Data Science\u2014Ministry of Education, School of Statistics, East China Normal University , Zhongshan North Road 3663, Shanghai 200062 ,","place":["China"]},{"name":"Shanghai Institute of Wildlife Epidemics, East China Normal University , Dongchuan Road 500, Shanghai 200062 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3381-2561","authenticated-orcid":false,"given":"Jun","family":"Wu","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University , Dongchuan Road 500, Shanghai 200241 ,","place":["China"]},{"name":"Shanghai Institute of Wildlife Epidemics, East China Normal University , Dongchuan Road 500, Shanghai 200062 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