Metataxonomic analysis of the uterine microbiota associated with low fertility in dairy cows using endometrial tissues prior to first artificial insemination

Abstract

Abstract Background: The deterioration in reproductive performance associated with low fertility leads to significant economic losses in dairy farms. Some causes of low fertility have not been identified and adequate countermeasures have not been undertaken. In recent years, the uterine microbiota has begun to attract attention as a possible cause of unexplained low fertility. This study analyzed the uterine microbiota associated with low fertility in dairy cows by 16S rRNA gene amplicon sequencing using endometrial biopsies sampled from cows that had passed the voluntary waiting period before the first artificial insemination (AI). Results: First, the uterine microbiota of 69 cows from four farms was analyzed regarding parity and AI frequency to conception, together with factors including housing style and feeding management, as each farm was managed differently. The analysis of microbial diversity revealed differences with respect to feeding management and housing style, but not parity and AI frequency. Next, to avoid the effect of housing style and feeding management, we performed the microbiota analysis in relation to parity and AI frequency in 31 cows from one farm. According to the microbiota diversity analysis, the weighted UniFrac beta diversity metric was correlated with AI frequency, but not with parity. A differential abundance analysis of AI frequency found that the abundance of the Arcobactergenus was increased, whereas the co-occurrence network analysis showed that Arcobacter cooperated with several other bacterial taxonomy units. A comparison of the network of the co-occurrence abundance patterns of normal and low-fertility cows (£3 and ³4 AIs, respectively) showed that bacterial associations related to low fertility, including the Arcobacter association, were observed in low-fertility cows. Finally, the examination of the ratio of the Arcobacter-hub model among the tested farms revealed that it was present to a certain extent, despite the skew toward certain farms. Thus, the Arcobacter genus may be key bacteria in the network module for low infertility in certain farms. Conclusion: This study provided new insights into the relevance of the uterine microbiota as a cause of low fertility, which significantly reduces cows’ reproductive performance.