{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T04:32:13Z","timestamp":1786422733329,"version":"build-2736575974"},"reference-count":43,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T00:00:00Z","timestamp":1786406400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Oral Health"],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Chlorhexidine is a standard antiseptic in periodontal therapy, yet its long-term impact on the commensal oral microbiota and antimicrobial resistance remains unclear.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objective<\/jats:title>\n                    <jats:p>This study evaluated the ecological effects of 0.06% chlorhexidine toothpaste on the salivary microbiota of healthy individuals, focusing on taxonomic composition, functional shifts, and prevalence of predicted antimicrobial resistance pathways.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>This study was designed as a prospective, single-arm interventional trial to evaluate the temporal dynamics of the oral microbiota. Saliva samples were collected from eleven healthy participants at three specific time points: baseline (following a 4-week run-in period using a reference fluoride toothpaste), intervention (after 12 weeks of using 0.06% chlorhexidine digluconate toothpaste), and washout (after a subsequent 12-week period using the reference fluoride toothpaste). Sequencing targeted the 16S rRNA V3\u2013V4 region.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Alpha diversity remained stable throughout the study. However, beta diversity analysis revealed significant shifts in community structure, which were most pronounced between the intervention and washout phases. We identified forty-one differentially abundant metabolic pathways, including a significant downregulation of predicted beta-lactam resistance pathways during the washout period. While chlorhexidine did not increase predicted resistance-related pathways, delayed compositional shifts toward gram-negative taxa were observed at the end of the 12-week washout period.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>These findings suggest that 0.06% chlorhexidine is not ecologically neutral, and dental professionals should carefully consider the appropriateness of chlorhexidine for long-term use.<\/jats:p>\n                    <jats:p>\n                      <jats:bold>Clinical Trial Registration:<\/jats:bold>\n                      <jats:ext-link>ClinicalTrials.gov<\/jats:ext-link>\n                      , NCT07570927.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/froh.2026.1887909","type":"journal-article","created":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T04:22:00Z","timestamp":1786422120000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Delayed shifts in salivary microbiota composition following long-term use of 0.06% chlorhexidine toothpaste"],"prefix":"10.3389","volume":"7","author":[{"given":"Veronika","family":"Chuchmova","sequence":"first","affiliation":[{"name":"Department of Public Health, Faculty of Medicine, Masaryk University","place":["Brno, Czechia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krist\u00fdna","family":"Brod\u00edkov\u00e1","sequence":"additional","affiliation":[{"name":"Department of Public Health, Faculty of Medicine, Masaryk University","place":["Brno, Czechia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martina","family":"Zapletalova","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Faculty of Science, Masaryk University","place":["Brno, Czechia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Lindholm","sequence":"additional","affiliation":[{"name":"Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet","place":["Stockholm, Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Krsek","sequence":"additional","affiliation":[{"name":"Department of Public Health, Faculty of Medicine, Masaryk University","place":["Brno, Czechia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,11]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1038\/sj.bdj.2016.865","article-title":"The oral microbiome \u2013 an update for oral healthcare professionals","volume":"221","author":"Kilian","year":"2016","journal-title":"Br Dent J"},{"key":"B2","doi-asserted-by":"publisher","first-page":"42","DOI":"10.3934\/microbiol.2018.1.42","article-title":"Oral microbiome and health","volume":"4","author":"Sharma","year":"2018","journal-title":"AIMS Microbiol"},{"key":"B3","doi-asserted-by":"publisher","first-page":"201","DOI":"10.2334\/JOSNUSD.16-0856","article-title":"The oral microbiome and human health","volume":"59","author":"Yamashita","year":"2017","journal-title":"J Oral Sci"},{"key":"B4","doi-asserted-by":"publisher","first-page":"1069","DOI":"10.1007\/s10266-025-01269-0","article-title":"Development of oral dysbiosis following use of antimicrobial mouthwashes: a systematic review","volume":"114","author":"Jayanandan","year":"2025","journal-title":"Odontology"},{"key":"B5","doi-asserted-by":"publisher","first-page":"103768","DOI":"10.1016\/j.jdent.2021.103768","article-title":"Effects of chlorhexidine mouthwash on the oral microbiome","volume":"113","author":"Brookes","year":"2021","journal-title":"J Dent"},{"key":"B6","doi-asserted-by":"publisher","first-page":"103497","DOI":"10.1016\/j.jdent.2020.103497","article-title":"Current uses of chlorhexidine for management of oral disease: a narrative review","volume":"103","author":"Brookes","year":"2020","journal-title":"J Dent"},{"key":"B7","doi-asserted-by":"publisher","first-page":"CD008676","DOI":"10.1002\/14651858.CD008676.pub2","article-title":"Chlorhexidine mouthrinse as an adjunctive treatment for gingival health","volume":"2017","author":"James","year":"2017","journal-title":"Cochrane Database Syst Rev"},{"key":"B8","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1902\/jop.1991.62.11.649","article-title":"Reduction of salivary bacteria by pre-procedural rinses with chlorhexidine 0.12%","volume":"62","author":"Veksler","year":"1991","journal-title":"J Periodontol"},{"key":"B9","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1111\/J.1600-0765.1970.TB00696.X","article-title":"The effect of mouthrinses and topical application of chlorhexidine on the development of dental plaque and gingivitis in man","volume":"5","author":"L\u00f6e","year":"1970","journal-title":"J Periodontal Res"},{"key":"B10","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1016\/J.IDENTJ.2022.01.005","article-title":"Chlorhexidine in dentistry: pharmacology, uses, and adverse effects","volume":"72","author":"Poppolo Deus","year":"2022","journal-title":"Int Dent J"},{"key":"B11","year":""},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1038\/S41598-020-61912-4","article-title":"Effects of chlorhexidine mouthwash on the oral microbiome","volume":"10","author":"Bescos","year":"2020","journal-title":"Sci Rep"},{"key":"B13","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1111\/PRD.12393","article-title":"The oral microbiome: role of key organisms and complex networks in oral health and disease","volume":"87","author":"Sedghi","year":"2021","journal-title":"Periodontol 2000"},{"key":"B14","year":""},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01972-21","article-title":"Reduced chlorhexidine susceptibility is associated with tetracycline resistance tet genes in clinical isolates of Escherichia coli","volume":"66","author":"Royer","year":"2022","journal-title":"Antimicrob Agents Chemother"},{"key":"B16","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1007\/S10096-022-04403-W","article-title":"Increasing usage of chlorhexidine in health care settings: blessing or curse? A narrative review of the risk of chlorhexidine resistance and the implications for infection prevention and control","volume":"41","author":"Van den Poel","year":"2022","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"B17","doi-asserted-by":"publisher","first-page":"2349","DOI":"10.1007\/S10096-021-04292-5","article-title":"Chlorhexidine leads to the evolution of antibiotic-resistant Pseudomonas aeruginosa","volume":"40","author":"Tag ElDein","year":"2021","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"B18","doi-asserted-by":"publisher","first-page":"1885","DOI":"10.1038\/s41591-021-01552-x","article-title":"Reporting guidelines for human microbiome research: the STORMS checklist","volume":"27","author":"Mirzayi","year":"2021","journal-title":"Nat Med"},{"key":"B19","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1111\/PRD.12359","article-title":"Optimizing the quality of clinical studies on oral microbiome: a practical guide for planning, performing, and reporting","volume":"85","author":"Zaura","year":"2021","journal-title":"Periodontol 2000"},{"key":"B20","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1902\/JOP.1967.38.6.610","article-title":"The gingival index, the plaque index and the retention index systems","volume":"38","author":"L\u00f6e","year":"1967","journal-title":"J Periodontol"},{"key":"B21","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1093\/nar\/gks808","article-title":"Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies","volume":"41","author":"Klindworth","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"B22","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/NMETH.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat Methods"},{"key":"B23","doi-asserted-by":"publisher","first-page":"W310","DOI":"10.1093\/nar\/gkad407","article-title":"Microbiomeanalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data","volume":"51","author":"Lu","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"B24","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1038\/s41587-020-0548-6","article-title":"PICRUSt2 for prediction of metagenome functions","volume":"38","author":"Douglas","year":"2020","journal-title":"Nat Biotechnol"},{"key":"B25","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1038\/sj.bdj.4800959","article-title":"Tooth discolouration and staining: a review of the literature","volume":"190","author":"Watts","year":"2001","journal-title":"Br Dent J"},{"key":"B26","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1007\/s00784-025-06627-4","article-title":"Effects of chlorhexidine and a polyherbal mouthwash on the oral microbiome and user satisfaction: a randomized controlled trial","volume":"29","author":"Wattanawongwan","year":"2025","journal-title":"Clin Oral Investig"},{"key":"B27","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1016\/j.freeradbiomed.2019.05.010","article-title":"Dietary intake of inorganic nitrate in vegetarians and omnivores and its impact on blood pressure, resting metabolic rate and the oral microbiome","volume":"138","author":"Ashworth","year":"2019","journal-title":"Free Radic Biol Med"},{"key":"B28","doi-asserted-by":"publisher","first-page":"e00235","DOI":"10.14309\/ctg.0000000000000235","article-title":"Relationship of the esophageal microbiome and tissue gene expression and links to the oral microbiome: a randomized clinical trial","volume":"11","author":"Annavajhala","year":"2020","journal-title":"Clin Transl Gastroenterol"},{"key":"B29","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1038\/s41598-020-79875-x","article-title":"Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models","volume":"11","author":"Relvas","year":"2021","journal-title":"Sci Rep"},{"key":"B30","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1007\/s00784-024-05913-x","article-title":"Current clinical framework on nitric oxide role in periodontal disease and blood pressure","volume":"28","author":"Lima","year":"2024","journal-title":"Clin Oral Investig"},{"key":"B31","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/j.freeradbiomed.2012.11.013","article-title":"Physiological role for nitrate-reducing oral bacteria in blood pressure control","volume":"55","author":"Kapil","year":"2013","journal-title":"Free Radic Biol Med"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1128\/ecosalplus.esp-0001-2018","article-title":"Function and biogenesis of lipopolysaccharides","volume":"8","author":"Bertani","year":"2018","journal-title":"EcoSal Plus"},{"key":"B33","doi-asserted-by":"publisher","first-page":"1429692","DOI":"10.3389\/fmicb.2024.1429692","article-title":"Chlorhexidine digluconate mouthwash alters the oral microbial composition and affects the prevalence of antimicrobial resistance genes","volume":"15","author":"Bartsch","year":"2024","journal-title":"Front Microbiol"},{"key":"B34","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1038\/s41579-024-01075-5","article-title":"The oral\u2013gut microbiome axis in health and disease","volume":"22","author":"Kunath","year":"2024","journal-title":"Nat Rev Microbiol"},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.1038\/S41522-024-00565-X","article-title":"Multi-way modelling of oral microbial dynamics and host-microbiome interactions during induced gingivitis","volume":"10","author":"Van Der Ploeg","year":"2024","journal-title":"NPJ Biofilms Microbiomes"},{"key":"B36","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1111\/PRD.12362","article-title":"Microbial signatures of health, gingivitis, and periodontitis","volume":"86","author":"Abusleme","year":"2021","journal-title":"Periodontol 2000"},{"key":"B37","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1111\/JCPE.13793","article-title":"Subgingival microbiome in periodontal health, gingivitis and different stages of periodontitis","volume":"50","author":"Iniesta","year":"2023","journal-title":"J Clin Periodontol"},{"key":"B38","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1038\/ISMEJ.2014.114","article-title":"The subgingival microbiome of clinically healthy current and never smokers","volume":"9","author":"Mason","year":"2015","journal-title":"ISME J"},{"key":"B39","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1186\/S40168-022-01338-4","article-title":"Functional changes in the oral microbiome after use of fluoride and arginine containing dentifrices: a metagenomic and metatranscriptomic study","volume":"10","author":"Carda-Di\u00e9guez","year":"2022","journal-title":"Microbiome"},{"key":"B40","doi-asserted-by":"publisher","first-page":"105941","DOI":"10.1016\/J.JDENT.2025.105941","article-title":"Changes in oral microbiome in preschool children after using toothpaste with different fluoride concentrations","volume":"161","author":"Zhang","year":"2025","journal-title":"J Dent"},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.1080\/20002297.2022.2105022","article-title":"Application of fluoride disturbs plaque microecology and promotes remineralization of enamel initial caries","volume":"18","author":"Zhang","year":"2022","journal-title":"J Oral Microbiol"},{"key":"B42","doi-asserted-by":"publisher","first-page":"729","DOI":"10.1007\/S00248-020-01531-8","article-title":"Shifts in composition and activity of oral biofilms after fluoride exposure","volume":"80","author":"L\u00f3pez-L\u00f3pez","year":"2020","journal-title":"Microb Ecol"},{"key":"B43","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1007\/S00284-023-03198-Z","article-title":"Combination of cetylpyridinium chloride and chlorhexidine acetate: a promising candidate for rapid killing of gram-positive\/gram-negative bacteria and fungi","volume":"80","author":"Zhu","year":"2023","journal-title":"Curr Microbiol"}],"container-title":["Frontiers in Oral Health"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/froh.2026.1887909\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T04:22:01Z","timestamp":1786422121000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/froh.2026.1887909\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,11]]},"references-count":43,"alternative-id":["10.3389\/froh.2026.1887909"],"URL":"https:\/\/doi.org\/10.3389\/froh.2026.1887909","relation":{},"ISSN":["2673-4842"],"issn-type":[{"value":"2673-4842","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,11]]},"article-number":"1887909"}}