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 gestation of two ewes (Ewe1 and Ewe2) that spontaneously aborted. Ewe1’s vaginal microbiota contained high abundances of Histophilus, Staphylococcus, and Unclassified Pasteurellaceae. Most notable was the high abundance of Campylobacter in Ewe1’s vaginal microbiota following the abortion. Ewe2’s vaginal microbiota was characterized by high abundances of Pasteurella 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 (ANI) to the most abundant sheep-abortive C. jejuni clone in the US. 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.