Date of Graduation


Document Type


Degree Name

Master of Science in Animal Science (MS)

Degree Level



Animal Science


Jiangchao Zhao

Committee Member

Rick Rorie

Second Committee Member

Charles Rosenkrans

Third Committee Member

Michael Looper


Beef Heifer, Reproduction, Vaginal Microbiome


The greatest impact on profitability of a commercial beef operation is reproduction. In the human vaginal microbiome, dominance by Lactobacillus is a sign of reproductive health and fitness. In other species (non-human primates and ewes), Lactobacillus is found in low amounts and dominators of these microbial communities are considered to be pathogenic in humans. In beef heifers, little is known about the vaginal and fecal microbiota with respect to their relationship with fertility. To this end, we followed heifers through gestation to examine the dynamics of vaginal and fecal microbial composition throughout pregnancy.

Heifers were exposed to an estrus synchronization period, including 12 days of artificial insemination eligibility, and subsequently exposed to bulls for a 50 day breeding season. Vaginal samples were taken at pre-breeding (n=72), during the first (n=72), and second trimester (n=72) for all individuals, and third trimester for individuals with confirmed pregnancies (n=56). Fecal samples were taken at pre-breeding (n=32) and during the first trimester (n=32) and included bred and open individuals. Next generation sequencing of the V4 region of the16S rRNA gene via the Illumina MiSeq platform was applied to all samples. Shannon indices and the number of observed OTUs were used as alpha-diversity measures resulting in no significant differences in fecal samples (P = 0.95, P = 0.66) and significant differences for vaginal samples due to pregnancy status and/or time (P = 0.0056, P = 0.0015). No differences in beta-diversity were seen in vaginal or fecal samples regarding pregnancy status and/or time. Random Forest was used to identify predictors of pregnancy status and/or time in fecal and vaginal samples and included but are not limited to: Histophilus, Paludibacter, unclassified Ruminococcaceae and Bacteroides. In conclusion, pregnancy status and/or time period altered alpha-diversity measures in vaginal samples. No changes due to pregnancy status were seen in alpha-diversity measures of fecal samples or beta-diversity measures in fecal and vaginal samples. Random Forest can be used to identify OTUs predictive of pregnancy status and gestational stage in vaginal and fecal samples.