Microbial signatures of the vaginal microbiome associated with pregnancy outcome in central Anatolian Merino sheep.

Reproductive efficiency is a key determinant of sustainability and profitability in sheep farming systems; however, the role of the vaginal microbiome in shaping pregnancy outcomes remains insufficiently understood. This study aimed to characterise the vaginal microbial communities of Central Anatolian Merino sheep using 16S rRNA gene amplicon sequencing and to explore their potential association with reproductive success. Vaginal samples were collected from 20 healthy ewes (10 non-pregnant (G1), that failed to conceive and returned to oestrus and 10 pregnant (G2), conceived at first service) with comparable physiological characteristics before breeding, followed by high-throughput amplicon sequencing to comprehensively profile the bacterial community structure. Comparative analyses were conducted between pregnant and non-pregnant animals to identify microbial patterns linked to pregnancy outcomes. The vaginal microbiome exhibited a diverse yet structured taxonomic composition across both groups, dominated by members of Bacillota (44.8% in G1 and 45.6% in G2), Actinomycetota (12.0% in G1 and 9.3% in G2), Pseudomonadota (6.6% in G1 and 6.2% in G2) and Bacteroidota (5.6% in G1 and 5.9% in G2). Alpha diversity did not differ significantly between groups (Wilcoxon rank-sum test, p > 0.05 across all indices), and beta diversity showed no significant separation (PERMANOVA, R2 = 0.055, p = 0.38), indicating substantial community overlap. Differential abundance analysis (edgeR) identified 23 taxa that differed between groups (FDR < 0.05), suggesting that reproductive outcomes may be influenced by subtle ecological shifts rather than large-scale microbial restructuring. Collectively, these findings provide novel insights into the vaginal microbial ecology of Central Anatolian Merino sheep and identify candidate microbial signatures that may warrant further investigation as potential correlates of fertility. Given the observational design and limited sample size, these associations should be interpreted as preliminary and hypothesis-generating. By advancing our understanding of host-microbiome interactions within the reproductive tract, this study establishes a foundation for microbiome-informed strategies aimed at improving reproductive performance and supporting sustainable sheep production.