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ARS Home » Plains Area » Miles City, Montana » Livestock and Range Research Laboratory » Research » Publications at this Location » Publication #431931
Research Project: Identifying and Mitigating Factors that Limit Beef Production Efficiency

Location: Livestock and Range Research Laboratory

Title: Vaginal microbiome is associated with breed and pregnancy status in beef cattle

Author
item FRAGOMENI, BRENO - University Of Connecticut
item HIRD, SARAH - University Of Connecticut
item Zezeski, Abigail
item Geary, Thomas
item MCCOSKI, SARAH - Montana State University
item Hay, El Hamidi

Submitted to: Animals
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/9/2026
Publication Date: 3/10/2026
Citation: Fragomeni, B., Hird, S., Zezeski, A.L., Geary, T.W., Mccoski, S., Hay, E.A. 2026. Vaginal microbiome is associated with breed and pregnancy status in beef cattle. Animals. 16(6). Article 874. https://doi.org/10.3390/ani16060874.
DOI: https://doi.org/10.3390/ani16060874

Interpretive Summary: Reproductive failure in cattle is a large economic burden to cattle production, therefore identifying factors that affect fertility is important. In this study, vaginal microbiomes of 74 beef cows from three genetic groups (Angus, Hereford Line 1, and crossbreds) were examined using 16S rRNA sequencing. The Line 1 cows differed significantly from the other groups in multiple diversity measures. Moreover, pregnancy status influenced diversity within Line 1. Overall microbial community composition was affected by genetic group and pregnancy status. Each breed had distinct OTU profiles; Line 1 had higher Ureaplasma and Mycoplasma, and some uncultured bacteria were more common in non-pregnant cows. The findings show breed- and pregnancy-associated differences in vaginal microbiomes and warrant further research to determine drivers and fertility associations.

Technical Abstract: Reproductive efficiency is vital for livestock productivity, with reproductive failure being a major cause of cow culling in beef and dairy operations. Due to the complexity and low heritability of reproductive traits, further investigation into genetic and non-genetic factors is essential. The hosts’ microbiome plays a crucial role in vertebrate biology, including reproduction, potentially serving as a biomarker for fertility. This study explored the relationship between vaginal microbiome profiles and fertility 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 14 out of 22 different indicators of diversity, evenness and dominance. While pregnancy status also significantly influenced the Line 1 group in the Fisher and Shannon diversity indexes. PERMANOVA analysis indicated that genetic groups and pregnancy status affected group 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 genera 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. These results suggest variation in vaginal microbiomes across breeds and pregnancy status, emphasizing the need for further research to identify factors affecting these changes.