The cervical microbiome of ewe breeds with known divergent fertility following artificial insemination with frozen-thawed semen

The use of artificial insemination (AI) with frozen-thawed semen in sheep is limited internationally due to low pregnancy rates. An exception is Norway, where high success rates routinely occur following vaginal deposition of frozen-thawed semen during natural estrus. Previous research suggests that breed-specific differences in pregnancy rates may result from impaired cervical sperm transport. This study compared cervical microbiomes among sheep breeds with known differences in pregnancy rates after AI. Cervical samples were collected from Suffolk (low fertility) and Belclare (medium fertility) breeds in Ireland, and Norwegian white sheep (NWS) and Fur breeds (both high fertility) in Norway, during the follicular phase of both natural and synchronized estruses, and the luteal phase of synchronized estrus. Amplicon sequencing revealed significantly higher bacterial abundance during the follicular phase in the low-fertility Suffolk breed compared to high-fertility breeds. Alpha diversity was higher in Suffolk and Belclare breeds, especially during the natural follicular phase, coinciding with pronounced beta diversity differences among breeds. Genus Histophilus was the top feature leading to microbial differences between ewe breeds and types of cycle. Ewe breed was the main driver of cervical microbial composition; increased microbial load in lower-fertility breeds may negatively impact sperm survival/transport, hampering AI success.