Characterization of the Vaginal Bacterial Microbiota of Sheep Exhibiting Abortion or Repeat Breeder Syndrome

• The vaginal microbiota of aborted and repeat breeder sheep (RBS) were characterized. • Pathogens are still the main ones causing abortion in ewes. • Pasteurellaceae had been listed as the key factor to RBS. • Vaginal microbial diversity in ovine plays a crucial role in reproductive regulation. Research on the microbiome’s impact on abortion and repeat breeder syndrome (RBS) in sheep is lacking, despite the fact that the vaginal bacterial microbiota is related to their reproductive performance. To compare ewe vaginal bacterial microbial communities, vaginal swabs were randomly taken from aborted ewes (A), repeat breeder ewes (RB), and healthy ewes (H), and 16S rRNA gene Illumina MiSeq amplicon sequencing was performed after DNA was extracted. Six common pathogens associated with reproductive disease were detected by PCR. Differences existed in alpha diversity between group A and group H ( p 0.05), the vagina of group H had a greater number of OTUs than group A and group RB, and there were also differences in the dominant genera within each group. Pathogenic bacteria ( Campylobacter jejuni, Chlamydia abortus, Listeria monocytogenes , and Brucella melitensis ) were detected in group A. Furthermore, changes in the relative abundance of bacterial genera such as Streptobacillus, unclassified Dysgonomonadaceae, Histophilus, unclassified Pasteurellaceae , and unclassified Leptotrichiaceae were observed in repeat breeder ewes; Pasteurellaceae was considered as the key factor to RBS. These findings suggest that the microbial diversity in the vagina of Hu sheep played a crucial role in reproductive regulation. Pathogens such as Brucella, Chlamydia are the main ones causing abortion in ewes, and the potential bacterial biomarkers could be discovered, and that would help prevent abortion or RBS.