trichomonosis is a venereal disease responsible for extensive economic losses. Tritrichomonas foetus, deposited during copulation, adheres to the vaginal mucosa where it proliferates. The vaginal bacterial microbiota protects the mucosa by colonization resistance. We sought to describe the bovine vaginal microbiota using metagenomics; contrasting between oestrus and dioestrus; and the interaction between the pathogen and the resident bacterial community. Six heifers were divided into control and infected groups. Using endometrial guarded swabs, three cranial vaginal samples were taken on days 1, 11 and 21 of their reproductive cycle, totalling eighteen samples. The DNA of the samples were extracted and the V3-V4 region of the 16S rRNA gene amplified prior to next-generation sequencing, which provided over a million high-quality reads. The vaginal bacterial microbiota of heifers were populated by organisms of the phyla Tenericutes, Proteobacteria, Firmicutes, Actinobacteria and Bacteriodetes. The control oestrus heifers were dominated by the phyla Tenericutes and Proteobacteria, represented by the families Mycoplasmataceae and Pasteurellaceae, respectively. The Shannon entropy (alpha diversity) were higher in oestrus than in dioestrus. Analysis of beta diversity via PERMANOVA did not reveal significant differences between heifers in oestrus and in dioestrus. However, the abundance of the family Mycoplasmataceae appeared to be affected by cycle stage (p<0.05). Analysis of the microbiota in the T. foetus infected heifers revealed a significantly higher alpha diversity compared to the controls in the corresponding stages of the oestrus cycle. Analysis of beta diversity via PERMANOVA revealed significant (p<0.1) differences between the two sample groups. The infected groups were found to have significantly less Mycoplasmataceae, and an increase in the families Bacillaceae, Ruminococcaceae, Propionibacteria, Lachnospiraceae, Paenibacillaceae and Prevotellaceae. The use of a culture-independent method expanded the knowledge of, and illustrated the substantial influence of, a few organisms on the bovine vaginal microbiota. The sex hormones may have influenced the microbiota. The introduction of T. foetus caused a dramatic change to the vaginal microbiota and an increase in the bacterial diversity.