Vaginal host–microbe signatures linked to placental outcomes in mares

BACKGROUND: Ascending placentitis is a leading cause of late-term pregnancy loss in mares. Although pathogens are presumed to ascend from the caudal reproductive tract, the association between the vaginal microbiome and placentitis has not been systematically examined. OBJECTIVES: To characterise microbial and host gene expression in the equine vagina during gestation and to identify taxa or transcripts that were associated with the presence of an abnormal placenta at birth. STUDY DESIGN: Prospective, paired observational study. METHODS: Vaginal wall swabs were collected from 49 multiparous Thoroughbred mares at days 42-46 and 118-133 of gestation (first and second trimester). Pregnancies were monitored to term, and placentas were classified as normal (healthy) or abnormal. Complete data was available for 37 mares, and 13 were included in this study: normal (n = 6), abnormal (n = 5), and ascending placentitis (n = 2). Total RNA underwent deep dual RNA-sequencing. Alpha- and beta-diversity metrics, differential expression, and microbe-host correlation analyses were performed. RESULTS: Global vaginal microbial diversity did not differ between mares with healthy or abnormal placentas. Several microbes from the phyla Actinomycetota and Pseudomonadota showed altered activity in mares with abnormal placentas. Vaginal transcriptome showed a subtle inflammatory response in the second trimester in the abnormal placenta group in the absence of clinical signs. Correlation analysis suggested an interaction between bacterial survival and virulence genes and host inflammation and apoptosis genes. MAIN LIMITATIONS: Samples were obtained from clinical cases, limiting the availability of a complete history. CONCLUSIONS: Although overall vaginal microbial diversity was similar between outcome groups, distinct host vaginal transcriptional and microbial activity signatures distinguished mares with an abnormal placenta at birth. These findings warrant targeted investigation of the vaginal immune response and bacterial virulence factors as early biomarkers and therapeutic targets.