Analysis of the sheep (Ovis aries) vaginal microbiota preceding spontaneous abortion: a pilot study

Little is known regarding the vaginal microbiota of sheep that undergo spontaneous abortions. The aim of this pilot study was to characterize, using 16S rRNA gene sequencing and shotgun metagenomics, the vaginal microbiota throughout the gestation of two ewes (Ewe1 and Ewe2) that spontaneously aborted. To achieve this, weekly vaginal swabs were collected from the ewes prior to breeding until pregnancy testing; thereafter, biweekly swabs were collected until the spontaneous abortion occurred. Based on the 16S rRNA sequencing data, Ewe1's vaginal microbiota, overall, contained high abundances of Histophilus (12.9% relative abundance), Staphylococcus (10.8% relative abundance) and Unclassified Pasteurellaceae (8.7% relative abundance). Most notable was the high abundance of Campylobacter following the abortion in Ewe1's vaginal microbiota. Ewe2's vaginal microbiota was characterized by high abundances of Pasteurella (41.7% relative abundance) throughout gestation. Shotgun metagenomic sequencing produced two high-quality metagenome-assembled genomes (MAGs), identified as Campylobacter jejuni and Histophilus somni. The C. jejuni MAG had 99.95% average nucleotide identity to the most abundant sheep abortive C. jejuni clone in the USA. The H. somni MAG was most similar to a pathogenic H. somni strain and contained genes that contribute to serum resistance and sialic acid utilization. The results presented here demonstrate the need for continued research into the vaginal microbiota, specifically to identify potential predictors of spontaneous abortion.