{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T14:10:33Z","timestamp":1785247833339,"version":"3.55.0"},"reference-count":69,"publisher":"Wiley","issue":"2","license":[{"start":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T00:00:00Z","timestamp":1762819200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T00:00:00Z","timestamp":1762819200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100008211","name":"Association France Parkinson","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008211","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Oral Microbiology"],"published-print":{"date-parts":[[2026,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Although the species is extensively studied, limited data are available on antiphage defense systems (APDSs) in\n                    <jats:italic>Streptococcus mutans<\/jats:italic>\n                    . The present study aimed to explore the diversity and the occurrence of APDSs and to search for prophages in the genomes of clinical isolates of\n                    <jats:italic>S. mutans<\/jats:italic>\n                    using bioinformatics tools.\n                  <\/jats:p>\n                  <jats:p>\n                    Forty\u2010four clinical isolates of\n                    <jats:italic>S. mutans<\/jats:italic>\n                    were obtained from saliva samples of people with Parkinson's disease. Genomic DNA was extracted, sequenced using Illumina MiSeq technology, and analyzed for the presence of defense systems using DefenseFinder and PADLOC. CRISPR\u2010Cas systems were characterized using CRISPRCasFinder, and prophages were detected by the PhiSpy pipeline from RAST. AcrFinder and AcrHub were used to identify anti\u2010CRISPR proteins.\n                  <\/jats:p>\n                  <jats:p>\n                    Each strain harbored between 6 and 12 APDS, with restriction\u2010modification systems being the most prevalent, followed by the MazEF toxin\u2013antitoxin system and CRISPR\u2010Cas systems. Type II\u2010C CRISPR\u2010Cas systems were not identified here in\n                    <jats:italic>S. mutans<\/jats:italic>\n                    . Novel variations in type II\u2010A signature protein Cas9 were identified, allowing their classification into four distinct groups. Variability in direct repeat sequences within the same CRISPR array was also observed, and 80% of the spacers were classified as targeting \u201cdark matter\u201d. A unique prophage, phi_37bPJ2, was detected, showing high similarity with previously described phages. The AcrIIA5 protein encoded by phi_37bPJ2 was conserved and suggested to remain functionally active.\n                  <\/jats:p>\n                  <jats:p>\n                    This study reveals the diversity of APDSs in\n                    <jats:italic>S. mutans<\/jats:italic>\n                    and the limited presence of prophages. The findings provide a foundation for future research on the evolutionary dynamics of these systems and their role in\n                    <jats:italic>S. mutans<\/jats:italic>\n                    adaptation to phage pressure.\n                  <\/jats:p>","DOI":"10.1111\/omi.70014","type":"journal-article","created":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T09:03:27Z","timestamp":1762851807000},"page":"57-68","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Defense Systems and Prophage Detection in\n                    <i>Streptococcus mutans<\/i>\n                    Strains"],"prefix":"10.1111","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6273-6289","authenticated-orcid":false,"given":"Olivier","family":"Claisse","sequence":"first","affiliation":[{"name":"University of Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR 1366, OENO, ISVV  Villenave d'Ornon France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5369-8938","authenticated-orcid":false,"given":"Cas","family":"Mosterd","sequence":"additional","affiliation":[{"name":"University of Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR 1366, OENO, ISVV  Villenave d'Ornon France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4175-6598","authenticated-orcid":false,"given":"Claire Le","family":"Marrec","sequence":"additional","affiliation":[{"name":"University of Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR 1366, OENO, ISVV  Villenave d'Ornon France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6087-2375","authenticated-orcid":false,"given":"Johan","family":"Samot","sequence":"additional","affiliation":[{"name":"University of Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, UMR 1366, OENO, ISVV  Villenave d'Ornon France"},{"name":"Department of Oral Surgery CHU Bordeaux  Bordeaux France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2025,11,11]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks406"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00284\u2010011\u20100025\u2010z"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa512"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2013.11.003"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102164\u20109\u201075"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00543\u201011"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.3390\/v13050825"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864\u2010016\u20102627\u20100"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae1082"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3893"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep08365"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/16.22.10881"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky425"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0138651"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365\u20102958.2008.06387.x"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.07726\u201011"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF01576015"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.3390\/v10110602"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10266\u2010025\u201001078\u20105"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.4057"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.108"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2019.10.017"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae671"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz548"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1007\/978\u20101\u201059745\u2010251\u20109_6"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859\u2010019\u20102906\u20102"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1177\/00220345820610021501"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1128\/iai.15.3.938\u2010944.1977"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365\u20102958.2002.02839.x"},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41522\u2010025\u201000773\u2010z"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1010065"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae814"},{"key":"e_1_2_9_34_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msy096"},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.828031"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.femsle.2005.09.045"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010025\u201062408\u20103"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae268"},{"key":"e_1_2_9_39_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0040913"},{"key":"e_1_2_9_40_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005944"},{"key":"e_1_2_9_41_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2022.09.017"},{"key":"e_1_2_9_42_1","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00235\u201020"},{"key":"e_1_2_9_43_1","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00185\u201021"},{"key":"e_1_2_9_44_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587\u2010020\u201000774\u20107"},{"key":"e_1_2_9_45_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0019543"},{"key":"e_1_2_9_46_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt1226"},{"key":"e_1_2_9_47_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.186072.114"},{"key":"e_1_2_9_48_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac400"},{"key":"e_1_2_9_49_1","doi-asserted-by":"publisher","DOI":"10.1039\/c5ay02550h"},{"key":"e_1_2_9_50_1","doi-asserted-by":"publisher","DOI":"10.3109\/1040841X.2013.804030"},{"key":"e_1_2_9_51_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.add8911"},{"key":"e_1_2_9_52_1","doi-asserted-by":"publisher","DOI":"10.3390\/genes16070842"},{"key":"e_1_2_9_53_1","doi-asserted-by":"publisher","DOI":"10.1128\/JB.02333\u201014"},{"key":"e_1_2_9_54_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574\u20106968.2009.01546.x"},{"key":"e_1_2_9_55_1","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01397\u201017"},{"key":"e_1_2_9_56_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