Vaginal Microbiome Is Associated with Breed and Pregnancy Status in Beef Cattle

Reproductive performance is a key determinant of overall livestock productivity. In both beef and dairy systems, reproductive failure represents a leading cause of cow culling. Reproductive traits are complex in nature and present a low heritability in general. Additionally, the collection of such phenotypes usually relies on indirect measures of fertility, such as conception success. Therefore, further investigation into genetic and non-genetic factors of reproductive traits in cattle is necessary. The hosts' microbiome plays a crucial role in vertebrate biology, including reproduction. We, therefore, hypothesize that microbiome indicators may serve as a biomarker of fertility. This study explored the relationship between vaginal microbiome profiles and pregnancy among three beef cattle genetic groups using field data. Vaginal swabs were collected from 74 cows at Fort Keogh, MT, including 23 Angus, 23 Hereford Line 1, and 28 crossbreds, and DNA was extracted and analyzed via 16S rRNA gene amplification. Significant differences in alpha diversity (p < 0.05) were found among Line 1 cows compared to Angus and crossbreds in many indicators of alpha diversity. Pregnancy status did not influence alpha diversity of samples significantly, but trends toward significance were observed. PERMANOVA analysis indicated that genetic groups and pregnancy status affected microbial composition (p < 0.05), but their interaction was not significant. Each genetic group showed unique compositions of operational taxonomic units (OTUs), with higher proportions of Ureaplasma and Mycoplasma families in Line 1. Additionally, variations in microbial communities were observed between pregnant and non-pregnant cows, with certain uncultured bacteria more prevalent in non-pregnant cows. While field data are useful for such studies and represent a real production system, better-designed experiments are necessary to validate findings and test hypotheses. These results suggest variation in vaginal microbiomes across breeds and pregnancy status, emphasizing the need for further research to identify factors affecting these changes.