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In\n              <jats:italic>Burkholderia pseudomallei<\/jats:italic>\n              , discrete genomic alterations and modulation of gene expression facilitate adaptation. Adapted variants of species within the\n              <jats:italic>Burkholderia cepacia<\/jats:italic>\n              complex (Bcc) often lose the pC3 virulence megaplasmid, impacting their colony morphology and their production of virulence factors. In this study, we characterize variants arising in\n              <jats:italic>Burkholderia ambifaria<\/jats:italic>\n              clinical isolates using proteomics and phenotypic tests and show that some of them have retained the pC3, indicating a distinct phase variation mechanism at play in this Bcc species. Interestingly, variants of\n              <jats:italic>B. ambifaria<\/jats:italic>\n              strains CEP0996 (pC3-null) and HSJ1 (pC3-positive) still share similarities in phenotypes controlled by the Cep quorum-sensing (QS) system. We further investigated the role of QS in\n              <jats:italic>B. ambifaria<\/jats:italic>\n              HSJ1 phase variation and confirmed that the Cep QS system is important for the emergence of variants. Given that DNA methylation is a key epigenetic factor regulating virulence factors in\n              <jats:italic>Burkholderia cenocepacia<\/jats:italic>\n              , we hypothesized that adenosine DNA methylation also governs phase variation in\n              <jats:italic>B. ambifaria<\/jats:italic>\n              HSJ1. By deleting the genes encoding putative adenosine DNA methyltransferases, we discovered that an orphan type II DNA methyltransferase inhibits the emergence of phase variants. This study is the first to demonstrate that quorum sensing and adenosine DNA methylation are two antagonistic systems independently controlling phase variation in\n              <jats:italic>B. ambifaria<\/jats:italic>\n              .\n            <\/jats:p>\n            <jats:sec>\n              <jats:title>IMPORTANCE<\/jats:title>\n              <jats:p>\n                Some\n                <jats:italic>Burkholderia<\/jats:italic>\n                species are pathogenic to plants, animals, or humans. In immunocompromised individuals, and people suffering from cystic fibrosis, infection from the\n                <jats:italic>Burkholderia cepacia<\/jats:italic>\n                complex (Bcc) can lead to \u201c\n                <jats:italic>cepacia<\/jats:italic>\n                syndrome.\u201d In northern Australia and southeast Asia, melioidosis caused by\n                <jats:italic>Burkholderia pseudomallei<\/jats:italic>\n                is prevalent among native population, particularly among people with diabetes, chronic lung or kidney disease or alcoholism.\n                <jats:italic>Burkholderia<\/jats:italic>\n                \u2019s phenotypic plasticity, including colony morphotype variation (CMV), enables rapid adaptation to diverse environments, enhancing its survival and pathogenicity. This study reveals phase variation as a new CMV mechanism within the Bcc group and is the first to report that quorum sensing and DNA methylation are involved in phase variation. Understanding the underlying mechanisms of CMV could lead to the development of targeted therapies against these highly antibiotic-tolerant bacteria.\n              <\/jats:p>\n            <\/jats:sec>\n          <\/jats:sec>","DOI":"10.1128\/jb.00531-24","type":"journal-article","created":{"date-parts":[[2025,2,14]],"date-time":"2025-02-14T14:00:41Z","timestamp":1739541641000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":4,"title":["Quorum sensing and DNA methylation play active roles in clinical\n            <i>Burkholderia<\/i>\n            phase variation"],"prefix":"10.1128","volume":"207","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9482-2360","authenticated-orcid":true,"given":"Pauline M. L.","family":"Coulon","sequence":"first","affiliation":[{"name":"Australian Institute for Microbiology and Infection, Faculty of Science, University of Technology Sydney","place":["Ultimo, Australia"]},{"name":"Centre Armand-Frappier Sant\u00e9 Biotechnologie, Institut National de la Recherche Scientifique","place":["Laval, Canada"]},{"name":"Department of Microbiology and Immunology, Doherty Institute, University of Melbourne","place":["Parkville, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4810-1030","authenticated-orcid":true,"given":"Marie-Christine","family":"Groleau","sequence":"additional","affiliation":[{"name":"Centre Armand-Frappier Sant\u00e9 Biotechnologie, Institut National de la Recherche Scientifique","place":["Laval, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8032-2154","authenticated-orcid":false,"given":"Abderrahman","family":"Hachani","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Doherty Institute, University of Melbourne","place":["Parkville, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8283-0643","authenticated-orcid":false,"given":"Matthew P.","family":"Padula","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Faculty of Science, University of Technology Sydney","place":["Ultimo, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0150-123X","authenticated-orcid":true,"given":"Timothy P.","family":"Stinear","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Doherty Institute, University of Melbourne","place":["Parkville, Australia"]},{"name":"Centre for Pathogen Genomics, University of Melbourne","place":["Melbourne, Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4609-0115","authenticated-orcid":true,"given":"Eric","family":"D\u00e9ziel","sequence":"additional","affiliation":[{"name":"Centre Armand-Frappier Sant\u00e9 Biotechnologie, Institut National de la Recherche Scientifique","place":["Laval, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.8221.1"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6976.2008.00113.x"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.3186\/jjphytopath.51.315"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1364-3703.2010.00676.x"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1094\/PDIS-93-9-0896"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00284-004-4354-z"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/159.5.890"},{"key":"e_1_3_4_9_2","first-page":"185","volume-title":"Oxford system of medicine","author":"Howe C","year":"1950","unstructured":"Howe C. 1950. 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