{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T14:07:04Z","timestamp":1787580424086,"version":"build-2736575974"},"reference-count":86,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T00:00:00Z","timestamp":1773100800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Research Cell, Noakhali Science and Technology University"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    <jats:italic>Vibrio cholerae<\/jats:italic>\n                    , a globally significant pathogen, causes both endemic and epidemic cholera and has also been associated with sporadic gastroenteritis and foodborne infections. Shrimp exports are a key source of revenue and employment in Bangladesh. However,\n                    <jats:italic>Vibrio<\/jats:italic>\n                    outbreaks pose serious public health and socio-economic risks through seafood consumption and the spread of antibiotic-resistant genes from aquaculture. The current study investigates the genomic and pathogenic features of the\n                    <jats:italic>V. cholerae<\/jats:italic>\n                    strain associated with seafood, with particular focus on the aquaculture environment of Bangladesh. Using Oxford Nanopore long-read sequencing technology, whole-genome sequencing (WGS) was performed on\n                    <jats:italic>V. cholerae<\/jats:italic>\n                    strain SU129B isolated from pacific white shrimp in Noakhali, Bangladesh, to explore its genetic diversity, antimicrobial resistance, and virulence determinants. The assembled genome exhibited high completeness (93.08%) and contiguity (N50\u2009=\u20091), along with minimal contamination (1.33%). Average nucleotide identity (ANI) analysis showed 98.13% similarity with the reference\n                    <jats:italic>V. cholerae<\/jats:italic>\n                    strain RFB16, confirming species-level identification. Functional and pathway analyses indicated that the strain possesses a complex network of genes and metabolic systems that contribute to its survival in diverse environments. Analysis of the genome also revealed several biosynthetic gene clusters associated with the production of secondary metabolites, which contribute to osmotic tolerance, and metal acquisition. The genome also harbored multiple antibiotic resistance genes, which confer resistance via efflux systems, target modification, and membrane adaptation mechanisms. Pangenome analysis revealed 8,964 genes, including 2,085 core genes, 429 soft-core genes, 1,431 shell genes, and 5,019 cloud genes, demonstrating considerable genetic diversity and adaptability. Phylogenetic analysis showed a close evolutionary relationship between the shrimp and clinical strains, suggesting possible genome conservation across environmental and clinical isolates. The findings demonstrate that\n                    <jats:italic>V. cholerae<\/jats:italic>\n                    strain SU129B can evolve in aquaculture environments and may serve as a reservoir for virulence and multidrug resistance.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0344787","type":"journal-article","created":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T17:34:16Z","timestamp":1773164056000},"page":"e0344787","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["Genomic and phylogenomic exploration of Vibrio cholerae strain SU129B isolated from Penaeus vannamei: Resistance, virulence, and evolutionary dynamics in bangladeshi aquaculture"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6509-9740","authenticated-orcid":true,"given":"Mohammad Sharif","family":"Uddin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazi","family":"Chamonara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0055-1895","authenticated-orcid":true,"given":"Md. Habib Ullah","family":"Masum","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Afifa","family":"Siddiqua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2516-8689","authenticated-orcid":true,"given":"Imam","family":"Hossain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sumaia","family":"Sultana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sajedul","family":"Islam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,3,10]]},"reference":[{"key":"pone.0344787.ref001","doi-asserted-by":"crossref","unstructured":"Haque ZF, Islam MS, Sabuj AAM, Pondit A, Sarkar AK, Hossain MG. Molecular detection and antibiotic resistance of Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio alginolyticus from shrimp (Penaeus monodon) and shrimp environments in Bangladesh. 2023;2023(1):5436552.","DOI":"10.1155\/2023\/5436552"},{"issue":"4","key":"pone.0344787.ref002","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1080\/10408398.2017.1384715","article-title":"Vibrio species involved in seafood-borne outbreaks (Vibrio cholerae, V. parahaemolyticus and V. vulnificus): Review of microbiological versus recent molecular detection methods in seafood products","volume":"59","author":"M Bonnin-Jusserand","year":"2019","journal-title":"Crit Rev Food Sci Nutr"},{"issue":"1","key":"pone.0344787.ref003","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1038\/s41572-018-0005-8","article-title":"Vibrio spp. infections","volume":"4","author":"C Baker-Austin","year":"2018","journal-title":"Nature Reviews Disease 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Microbiol"},{"issue":"45","key":"pone.0344787.ref007","doi-asserted-by":"crossref","first-page":"17801","DOI":"10.1073\/pnas.0705599104","article-title":"Viable but nonculturable Vibrio cholerae O1 in biofilms in the aquatic environment and their role in cholera transmission","volume":"104","author":"M Alam","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pone.0344787.ref008","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00483-18","article-title":"Biofilms comprise a component of the annual cycle of Vibrio cholerae in the Bay of Bengal estuary","volume":"9","author":"M Sultana","year":"2018","journal-title":"mBio"},{"issue":"4","key":"pone.0344787.ref009","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1128\/mr.56.4.622-647.1992","article-title":"Structure and function of cholera toxin and the related Escherichia coli heat-labile enterotoxin","volume":"56","author":"BD Spangler","year":"1992","journal-title":"Microbiol 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F","year":"2024"},{"key":"pone.0344787.ref013","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2023\/5436552","article-title":"Molecular Detection and Antibiotic Resistance of Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio alginolyticus from Shrimp (Penaeus monodon) and Shrimp Environments in Bangladesh","volume":"2023","author":"ZF Haque","year":"2023","journal-title":"Aquaculture Research"},{"issue":"1","key":"pone.0344787.ref014","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/j.1574-6968.2009.01512.x","article-title":"Transfer of plasmid-mediated resistance to tetracycline in pathogenic bacteria from fish and aquaculture environments","volume":"293","author":"E Guglielmetti","year":"2009","journal-title":"FEMS Microbiol Lett"},{"key":"pone.0344787.ref015","author":"P Serrano","year":"2005","journal-title":"Responsible Use of Antibiotics in Aquaculture"},{"issue":"2","key":"pone.0344787.ref016","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/j.ijantimicag.2018.03.010","article-title":"Antimicrobial resistance in aquaculture: Current knowledge and alternatives to tackle the problem","volume":"52","author":"L Santos","year":"2018","journal-title":"Int J Antimicrob Agents"},{"key":"pone.0344787.ref017","volume-title":"Selection and application of methods for the detection and enumeration of human-pathogenic halophilic vibrio spp. in seafood: guidance","author":"Organization WH","year":"2016"},{"key":"pone.0344787.ref018","author":"RE Buchanan","year":"1974","journal-title":"Bergey\u2019s manual of determinative bacteriology"},{"key":"pone.0344787.ref019","volume-title":"Bergey\u2019s manual of determinative bacteriology","author":"DH Bergey","year":"1994"},{"issue":"2","key":"pone.0344787.ref020","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1111\/jam.12056","article-title":"Development of a groEL gene-based species-specific multiplex polymerase chain reaction assay for simultaneous detection of Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus","volume":"114","author":"MT Hossain","year":"2013","journal-title":"J Appl Microbiol"},{"key":"pone.0344787.ref021","author":"JA Hindler","year":"2016","journal-title":"CLSI M45 2016"},{"key":"pone.0344787.ref022","unstructured":"EUCAST. Clinical breakpoints and dosing of antibiotics\u2014Version 16. 2026."},{"key":"pone.0344787.ref023","author":"I Lewis","year":"2024","journal-title":"Performance standards for antimicrobial susceptibility testing"},{"key":"pone.0344787.ref024","author":"R Wick","year":"2018","journal-title":"Porechop: adapter trimmer for Oxford Nanopore reads"},{"issue":"15","key":"pone.0344787.ref025","doi-asserted-by":"crossref","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","article-title":"NanoPack: visualizing and processing long-read sequencing data","volume":"34","author":"W De Coster","year":"2018","journal-title":"Bioinformatics"},{"issue":"5","key":"pone.0344787.ref026","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"M Kolmogorov","year":"2019","journal-title":"Nat 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Microbiol"},{"issue":"7","key":"pone.0344787.ref030","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"DH Parks","year":"2015","journal-title":"Genome Res"},{"issue":"12","key":"pone.0344787.ref031","article-title":"BUSCO: Assessing genomic data quality and beyond","volume":"1","author":"M Manni","year":"2021","journal-title":"Curr Protoc"},{"issue":"8","key":"pone.0344787.ref032","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"A Gurevich","year":"2013","journal-title":"Bioinformatics"},{"issue":"1","key":"pone.0344787.ref033","doi-asserted-by":"crossref","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic 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Res"},{"key":"pone.0344787.ref037","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkad326","article-title":"Proksee: in-depth characterization and visualization of bacterial genomes","volume":"51","author":"JR Grant","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"17","key":"pone.0344787.ref038","doi-asserted-by":"crossref","first-page":"5691","DOI":"10.1093\/nar\/gki866","article-title":"The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes","volume":"33","author":"R Overbeek","year":"2005","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pone.0344787.ref039","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1038\/s41929-018-0212-4","article-title":"A comprehensive metabolic map for production of bio-based chemicals","volume":"2","author":"SY Lee","year":"2019","journal-title":"Nat Catal"},{"issue":"11","key":"pone.0344787.ref040","doi-asserted-by":"crossref","first-page":"4286","DOI":"10.1128\/IAI.00207-11","article-title":"PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species","volume":"79","author":"JJ Gillespie","year":"2011","journal-title":"Infect Immun"},{"issue":"2","key":"pone.0344787.ref041","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1016\/j.cell.2014.06.034","article-title":"Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters","volume":"158","author":"P Cimermancic","year":"2014","journal-title":"Cell"},{"key":"pone.0344787.ref042","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkad344","article-title":"antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation","volume":"51","author":"K Blin","year":"2023","journal-title":"Nucleic Acids Research"},{"issue":"7","key":"pone.0344787.ref043","doi-asserted-by":"crossref","first-page":"3348","DOI":"10.1128\/AAC.00419-13","article-title":"The comprehensive antibiotic resistance database","volume":"57","author":"AG McArthur","year":"2013","journal-title":"Antimicrob Agents Chemother"},{"issue":"9","key":"pone.0344787.ref044","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/nrmicro1235","article-title":"Mobile genetic elements: the agents of open source evolution","volume":"3","author":"LS Frost","year":"2005","journal-title":"Nat Rev Microbiol"},{"issue":"18","key":"pone.0344787.ref045","doi-asserted-by":"crossref","DOI":"10.1128\/aem.00991-22","article-title":"mobileOG-db: a manually curated database of protein families mediating the life cycle of bacterial mobile genetic elements","volume":"88","author":"CL Brown","year":"2022","journal-title":"Appl Environ Microbiol"},{"issue":"8","key":"pone.0344787.ref046","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1080\/21505594.2014.995573","article-title":"Regulation of virulence gene expression","volume":"5","author":"MS Thomas","year":"2014","journal-title":"Virulence"},{"key":"pone.0344787.ref047","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gky999","article-title":"Victors: a web-based knowledge base of virulence factors in human and animal pathogens","volume":"47","author":"S Sayers","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"22","key":"pone.0344787.ref048","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"AJ Page","year":"2015","journal-title":"Bioinformatics"},{"key":"pone.0344787.ref049","doi-asserted-by":"crossref","first-page":"135371","DOI":"10.1016\/j.ijbiomac.2024.135371","article-title":"Application of lipopolysaccharide in establishing inflammatory models","volume":"279","author":"X Zhang","year":"2024","journal-title":"Int J Biol Macromol"},{"issue":"2","key":"pone.0344787.ref050","article-title":"TAM mediates adaptation of carbapenem-resistant Klebsiella pneumoniae to antimicrobial stress during host colonization and infection","volume":"17","author":"H-J Jung","year":"2021","journal-title":"PLoS Pathog"},{"issue":"3","key":"pone.0344787.ref051","doi-asserted-by":"crossref","first-page":"1411","DOI":"10.1128\/IAI.73.3.1411-1422.2005","article-title":"A Vibrio vulnificus type IV pilin contributes to biofilm formation, adherence to epithelial cells, and virulence","volume":"73","author":"RN Paranjpye","year":"2005","journal-title":"Infect Immun"},{"issue":"3","key":"pone.0344787.ref052","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1128\/MMBR.00015-14","article-title":"Microbial peptidyl-prolyl cis\/trans isomerases (PPIases): virulence factors and potential alternative drug targets","volume":"78","author":"CM \u00dcnal","year":"2014","journal-title":"Microbiol Mol Biol Rev"},{"issue":"9","key":"pone.0344787.ref053","doi-asserted-by":"crossref","DOI":"10.3390\/metabo12090818","article-title":"Degradation of xenobiotic pollutants: an environmentally sustainable approach","volume":"12","author":"R Miglani","year":"2022","journal-title":"Metabolites"},{"issue":"3","key":"pone.0344787.ref054","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1002\/cbic.201500474","article-title":"Aryl Polyenes, a Highly Abundant Class of Bacterial Natural Products, Are Functionally Related to Antioxidative Carotenoids","volume":"17","author":"TA Sch\u00f6ner","year":"2016","journal-title":"Chembiochem"},{"issue":"1","key":"pone.0344787.ref055","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/s41522-021-00226-3","article-title":"Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation","volume":"7","author":"I Johnston","year":"2021","journal-title":"NPJ Biofilms Microbiomes"},{"issue":"16","key":"pone.0344787.ref056","doi-asserted-by":"crossref","first-page":"5038","DOI":"10.1128\/AEM.01008-13","article-title":"Biosynthesis of the osmoprotectant ectoine, but not glycine betaine, is critical for survival of osmotically stressed Vibrio parahaemolyticus cells","volume":"79","author":"SY Ongagna-Yhombi","year":"2013","journal-title":"Appl Environ Microbiol"},{"issue":"6","key":"pone.0344787.ref057","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1128\/JB.182.6.1731-1738.2000","article-title":"Vibrio cholerae VibF is required for vibriobactin synthesis and is a member of the family of nonribosomal peptide synthetases","volume":"182","author":"JR Butterton","year":"2000","journal-title":"J Bacteriol"},{"issue":"1","key":"pone.0344787.ref058","doi-asserted-by":"crossref","first-page":"52","DOI":"10.3390\/pathogens14010052","article-title":"Genomic Insight into Vibrio Isolates from Fresh Raw Mussels and Ready-to-Eat Stuffed Mussels","volume":"14","author":"A Yibar","year":"2025","journal-title":"Pathogens"},{"issue":"3","key":"pone.0344787.ref059","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1039\/D4NP00048J","article-title":"The role and mechanisms of canonical and non-canonical tailoring enzymes in bacterial terpenoid biosynthesis","volume":"42","author":"Y Kakumu","year":"2025","journal-title":"Nat Prod Rep"},{"issue":"10","key":"pone.0344787.ref060","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1021\/ar00022a001","article-title":"Isocyanides and cyanides as natural products","volume":"25","author":"PJ Scheuer","year":"1992","journal-title":"Acc Chem Res"},{"issue":"3","key":"pone.0344787.ref061","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1039\/C8NP00052B","article-title":"Biosynthesis and chemical diversity of \u03b2-lactone natural products","volume":"36","author":"SL Robinson","year":"2019","journal-title":"Nat Prod Rep"},{"issue":"44","key":"pone.0344787.ref062","doi-asserted-by":"crossref","first-page":"14400","DOI":"10.1021\/ja8051365","article-title":"Beta-lactones as specific inhibitors of ClpP attenuate the production of extracellular virulence factors of Staphylococcus aureus","volume":"130","author":"T B\u00f6ttcher","year":"2008","journal-title":"J Am Chem Soc"},{"issue":"7","key":"pone.0344787.ref063","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1038\/nrmicro3047","article-title":"Fortifying the barrier: the impact of lipid A remodelling on bacterial pathogenesis","volume":"11","author":"BD Needham","year":"2013","journal-title":"Nat Rev Microbiol"},{"key":"pone.0344787.ref064","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1146\/annurev.biochem.76.010307.145803","article-title":"Lipid A modification systems in gram-negative bacteria","volume":"76","author":"CRH Raetz","year":"2007","journal-title":"Annu Rev Biochem"},{"issue":"3","key":"pone.0344787.ref065","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/ja.2008.120","article-title":"CRP regulator modulates multidrug resistance of Escherichia coli by repressing the mdtEF multidrug efflux genes","volume":"61","author":"K Nishino","year":"2008","journal-title":"J Antibiot (Tokyo)"},{"key":"pone.0344787.ref066","first-page":"203","article-title":"Acquired antibiotic resistance genes: an overview","volume":"2","author":"AHAM van Hoek","year":"2011","journal-title":"Front Microbiol"},{"issue":"4","key":"pone.0344787.ref067","doi-asserted-by":"crossref","DOI":"10.1128\/CMR.00088-17","article-title":"Mobile genetic elements associated with antimicrobial resistance","volume":"31","author":"SR Partridge","year":"2018","journal-title":"Clinical Microbiology Reviews"},{"issue":"3","key":"pone.0344787.ref068","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1002\/pro.3819","article-title":"Molecular mechanisms of vancomycin resistance","volume":"29","author":"PJ Stogios","year":"2020","journal-title":"Protein Sci"},{"issue":"9","key":"pone.0344787.ref069","doi-asserted-by":"crossref","first-page":"2233","DOI":"10.1128\/AAC.44.9.2233-2241.2000","article-title":"Efflux-mediated resistance to fluoroquinolones in gram-negative bacteria","volume":"44","author":"K Poole","year":"2000","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"pone.0344787.ref070","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1128\/AAC.00665-08","article-title":"Mechanisms accounting for fluoroquinolone resistance in Escherichia coli clinical isolates","volume":"53","author":"SK Morgan-Linnell","year":"2009","journal-title":"Antimicrob Agents Chemother"},{"issue":"11","key":"pone.0344787.ref071","doi-asserted-by":"crossref","first-page":"2792","DOI":"10.1128\/AAC.42.11.2792","article-title":"Fluoroquinolone resistance mutations in the parC, parE, and gyrA genes of clinical isolates of viridans group streptococci","volume":"42","author":"I Gonz\u00e1lez","year":"1998","journal-title":"Antimicrob Agents Chemother"},{"issue":"1","key":"pone.0344787.ref072","doi-asserted-by":"crossref","DOI":"10.1111\/1751-7915.14408","article-title":"Microbial evolution through horizontal gene transfer by mobile genetic elements","volume":"17","author":"M Tokuda","year":"2024","journal-title":"Microb Biotechnol"},{"issue":"9","key":"pone.0344787.ref073","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a025320","article-title":"Topoisomerase inhibitors: fluoroquinolone mechanisms of action and resistance","volume":"6","author":"DC Hooper","year":"2016","journal-title":"Cold Spring Harbor Perspectives in Medicine"},{"issue":"29","key":"pone.0344787.ref074","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2304378120","article-title":"ToxR activates the Vibrio cholerae virulence genes by tethering DNA to the membrane through versatile binding to multiple sites","volume":"120","author":"A Canals","year":"2023","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"12","key":"pone.0344787.ref075","doi-asserted-by":"crossref","first-page":"8167","DOI":"10.1128\/IAI.73.12.8167-8178.2005","article-title":"Iron and fur regulation in Vibrio cholerae and the role of fur in virulence","volume":"73","author":"AR Mey","year":"2005","journal-title":"Infect Immun"},{"issue":"22","key":"pone.0344787.ref076","doi-asserted-by":"crossref","first-page":"7482","DOI":"10.1128\/AEM.01564-07","article-title":"The cyclic AMP receptor protein modulates colonial morphology in Vibrio cholerae","volume":"73","author":"W Liang","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"pone.0344787.ref077","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.jmb.2012.03.028","article-title":"Characterization of Vibrio cholerae Hfq provides novel insights into the role of the Hfq C-terminal region","volume":"420","author":"HA Vincent","year":"2012","journal-title":"J Mol 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In Silico Functional Characterization of a Hypothetical Protein from Reveals a Novel-Adenosylmethionine-Dependent Methyltransferase Activity. 2023;17.","DOI":"10.1177\/11779322231184024"},{"issue":"5","key":"pone.0344787.ref086","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1111\/j.1574-6976.2011.00292.x","article-title":"Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches","volume":"35","author":"J Wiedenbeck","year":"2011","journal-title":"FEMS Microbiol Rev"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0344787","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T17:34:27Z","timestamp":1773164067000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0344787"}},"subtitle":[],"editor":[{"given":"Md. 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