The uterine microbiome shifts of mares during intra- and interspecies breeding

An extra-species model (donkey-to- and horse-to-mare) was designed to determine the effects of the male seminal microbiome on the mare uterine microbiome. The semen and uterine microbiomes were analyzed among seventy-five estrous cycles of mares (n=15) inseminated with a single fertile donkey or horse raw semen or infused with saline, donkey, or horse seminal plasma in a crossover design. After filtering and agglomeration, sequencing the full 16S gene resulted in the assignment of 99 taxa. Alpha diversity differed between donkey and horse semen, whereas beta diversity was similar across species. The most prevalent phyla in mare-cycles infused with donkey semen were Proteobacteria (50.3%), Actinobacteria (18%), and Firmicutes (29.8%); similarly, with the horse semen, Proteobacteria (62.5%), Actinobacteria (21.7%), and Firmicutes (12.3%) were the most abundant. The beta diversity of the uterus differed across the mare-cycles based on the type of infusion and on the presence of an embryo in both mare-cycles infused with donkey and horse semen. In conclusion, the semen microbiome varied between the two equids used in the study, and more importantly, the semen microbiome affected the mare uterine microbiome and suggested the presence of a temporary combined male and female microbiome.