Virtually all cows are infected with bacteria postpartum, and failure to control pathogenic bacterial growth leads to the establishment of disease. Our previous work using 16S rRNA gene sequencing showed that cows have an established uterine microbiota within 20 min of calving. Both cows that remain healthy and cows that develop metritis have sub-communities of bacteria that lead to the development of metritis and commensal sub-communities that are associated with uterine health. However, in cows that develop metritis, there is a dysbiosis in the microbial community in which pathogenic bacteria overtake the uterine commensals. We showed that bacterial relative abundance is similar between healthy and metritic cows up until 2 DPP, after which they deviate in favor of greater abundance of Bacteroides, Porphyromonas and Fusobacterium in cows that develop metritis. We recently confirmed our 16S metagenomic findings using quantitative PCR. At the time of metritis diagnosis (6 ± 2DPP), metritic cows had a greater absolute abundance of total bacteria, and greater abundance of Bacteroides pyogenes, Porphyromonas levii, and Fusobacterium necrophorum, the main species from the genera Bacteroides, Porphyromonas and Fusobacterium, respectively. Previous work using bacterial culture of the postpartum uterus or using PCR to target specific bacteria, pointed to an involvement of Escherichia coli and Trueperellapyogenes, in the pathogenesis or metritis. However, our work does not show an involvement of E. coli or T. pyogenes at the time of metritis diagnosis; therefore, our interpretation is that E. coli might be a pioneer pathogen that predisposes to uterine colonization by Bacteroides, Porphyromonas, and Fusobacterium, and that T. pyogenes would become more important later on, and would be mostly involved in the pathogenesis of endometritis. In summary, our work has increased our understanding of the uterine microbiota in health and disease, and can be used to guide the development of new prophylactic and therapeutic interventions.