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Phages are an important component of the periodontal microbiome, yet our understanding of periodontal phages remains limited. Here, we investigated oral periodontal phages using various advanced bioinformatics tools based on genomes of key periodontitis pathogens. Prophages were found to encode various auxiliary genes that potentially enhance host survival and pathogenicity, including genes involved in carbohydrate metabolism, antibiotic resistance, and immune modulation. We observed cross-species transmission among prophages with a complex network of phage-bacteria interactions. Our findings suggest that prophages play a crucial role in shaping the periodontal microbial ecosystem, influencing microbial community dynamics and the progression of periodontitis.<\/jats:p>\n            <jats:sec>\n              <jats:title>IMPORTANCE<\/jats:title>\n              <jats:p>In the context of periodontitis, the ecological dynamics of the microbiome are largely driven by interactions between bacteria and their phages. While the impact of prophages on regulating oral pathogens has been increasingly recognized, their role in modulating periodontal disease remains underexplored. This study reveals that prophages within key periodontitis pathogens contribute significantly to virulence factor dissemination, antibiotic resistance, and host metabolism. By influencing the metabolic capabilities and survival strategies of their bacterial hosts, prophages may act as critical regulators of microbial communities in the oral cavity. Understanding these prophage-mediated interactions is essential not only for unraveling the mechanisms of periodontal disease progression but also for developing innovative therapeutic approaches that target the microbial ecosystem at the genetic level. These insights emphasize the need for more comprehensive studies on the ecological risks posed by prophages in shaping microbial pathogenicity and resistance.<\/jats:p>\n            <\/jats:sec>\n          <\/jats:sec>","DOI":"10.1128\/msystems.00201-25","type":"journal-article","created":{"date-parts":[[2025,3,28]],"date-time":"2025-03-28T13:28:58Z","timestamp":1743168538000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":8,"title":["Unveiling the role of phages in shaping the periodontal microbial ecosystem"],"prefix":"10.1128","volume":"10","author":[{"given":"Fangfang","family":"Yao","sequence":"first","affiliation":[{"name":"State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology Wuhan University","place":["Wuhan, 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