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This research aims to identify the ewes\u2019 vaginal core bacterial community, examine the factors influencing bacterial composition, and to determine the association between vaginal bacteria and pregnancy success. By using a robust dataset comprising 331 multiparous ewes from three Spanish breeds (Latxa, Manchega, Rasa Aragonesa) across four herds, this study performed the sequencing of the hypervariable regions V3-V4 of the 16S ribosomal RNA gene and the identification of Amplicon Sequence Variants (ASV) to analyze the bacterial community. Our analysis revealed a core bacterial primarily consisting of the genera <jats:italic>Streptobacillus, Histophilus, Fusobacterium, Oceanivirga,<\/jats:italic> and <jats:italic>Parvimonas<\/jats:italic>. Alpha and beta diversity, as well as Random Forest analysis, identified that herd and breed were the main drivers of bacterial variability. PERMANOVA analysis also showed significant differences in bacterial composition and abundance associated with pregnancy outcomes. Notably, specific ASVs associated with <jats:italic>Fusobacterium<\/jats:italic>, <jats:italic>Leptotrichia<\/jats:italic>, <jats:italic>Histophilus<\/jats:italic>, <jats:italic>Escherichia,<\/jats:italic> and <jats:italic>Bacteroides<\/jats:italic> were predominantly found in non-pregnant ewes, while genera such as <jats:italic>Pseudomonas, Acinetobacter,<\/jats:italic> and <jats:italic>Brevundimonas<\/jats:italic> were more abundant in pregnant ewes. This study contributes to the knowledge about the critical roles of specific bacteria in determining reproductive success in sheep and provides novel insights about the importance of different factors involved in the composition of ewes\u2019 vaginal bacterial communities.<\/jats:p>","DOI":"10.1186\/s42523-025-00383-2","type":"journal-article","created":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T16:07:08Z","timestamp":1747238828000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Characterization of bacterial communities of ewe\u2019s vaginal tract and its potential impact on reproductive efficiency"],"prefix":"10.1186","volume":"7","author":[{"given":"E. 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Animal manipulations were performed according to the Spanish Policy for Animal Protection RD 53\/2013, which meets the European Union Directive 86\/609 about the protection of animals used in experimentation. We hereby confirm that the INIA Scientific Ethic Committee (IACUC) has approved this study. Written informed consent was obtained from the owners for the participation of their animals in this study.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"The authors dclare that they have no competing interest.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing of interests"}}],"article-number":"48"}}