Ovine Papillomavirus Type 1 DNA Positivity Is Associated with Distinct Uterine Microbial Communities in Mares During Estrus

Uterine flushings were collected from 45 apparently healthy mares during estrus from eight stud farms in Italy: one in Campania, five in Basilicata, and two in Calabria. Samples were analyzed using digital polymerase chain reaction (dPCR) and 16S rRNA gene amplicon sequencing. OaPV1 DNA was the only genotype detected by dPCR and was identified in 17 samples, while 28 samples were negative. Sequencing of 16S rRNA characterized and compared uterine microbiota and predicted metabolic pathways between OaPV1-positive and OaPV1-negative mares. Six major phyla were identified: Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, Fusobacteriota, and Synergistota. Although OaPV1-positive samples showed no significant differences in microbial richness, they exhibited significant alterations in community evenness and overall microbial structure across all tested metrics, with weighted UniFrac explaining the largest proportion of variance (R2 = 0.134). Differential abundance analysis identified 43 taxa across six phyla that differed between groups, including enrichment of potentially pathogenic genera (Murdochiella, Clostridia_UCG-014, and Cellulomonas) and depletion of potentially beneficial groups (Clostridia_vadinBB60_group and Taylorella). Functional prediction revealed 108 differentially represented KEGG pathways, mainly related to amino acid biosynthesis, carbohydrate and energy metabolism, and the TCA cycle. These findings suggest an association between OaPV1 status and uterine microbiota alterations. Further studies are warranted to investigate the potential bidirectional interplay between papillomavirus infection and reproductive tract dysbiosis.