Compositional and functional metabolic shifts of the endometrial microbiota in cows (Bos taurus) during the transition period: A metagenomic next-generation sequencing approach

Background: During the transition period of dairy cows (3 weeks before, and 3 weeks after, calving), significant alterations in feeding, housing and physiology of animals are observed, as are changes in the composition and abundance of the endometrial microbiota. The aim of the study was to evaluate changes in the composition and predicted metabolic pathways of the cow uterine microbiome in this transition period. Methods: Sampling of scrapings from the endometrial surface was conducted from clinically healthy cows (n = 3) in dynamics as follows: in the 10-day period before, and on Days 3, 5 and 20 after, calving. Total DNA from the samples was isolated, and the composition of the microbial community was assessed using targeted next-generation sequencing (NGS) technology. Based on NGS data, the dynamics of the predicted metabolic pathways of the microbiota were assessed. Results: Seven superphyla and phyla of microorganisms were found in the endometrial microbiota of cows during the transition period. Among them, the phylum Firmicutes (with a dominant class of Clostridia) and the superphylum Fusobacteriota (represented by a single class of Fusobacteriia) can be considered the dominant bacteria in the endometrium, with representation from 25.2 to 68.2% and from 12.3 to 51.1%, respectively. The microbiome composition underwent significant changes (p < 0.05) during the transition period. In particular, the high abundance of the Fusobacteriaceae family (up to 68.2%) in the uterus of clinically healthy cows was unexpected, given their potential association with the occurrence of metritis in cows. The numbers of microorganisms in two dominant classes Fusobacteriia and Clostridia showed generally opposite changes in their relative abundance during the transition period. The predicted functional potential level for 32 pathways in the endometrium changed (p < 0.05) in cows in the course of the transition period. On Day 3 postpartum, the activity of predicted pathways such as pyridoxal 5'-phosphate biosynthesis I and teichoic acid (poly-glycerol) biosynthesis lowered (p < 0.05). Conclusions: Microbiota composition and activity of predicted metabolic pathways in the cow endometrium underwent significant changes associated with different critical stages of the transition period. Even clinically healthy cows showed signs of dysbiotic disorders.