Metagenome shotgun sequencing allows insights into the functional potential of the vaginal microbiome associated with pelvic organ prolapse in sows

Abstract Pelvic organ prolapse (POP) is a leading cause for sow mortality in the United States. Recent work has evaluated biological factors associated with POP, and differences have been observed within the vaginal microbiota of sows at high risk using 16S rRNA gene amplicon sequencing. Additional functional studies are needed to better understand the relationship of dysbiosis of the vaginal microbiome with POP risk in sows. The current study’s objective was to provide information about the functional potential of the sow vaginal microbiome, and to identify candidate genes and organisms that may be associated with POP. For this, metagenome shotgun sequencing was conducted on DNA extracted from 16 vaginal swab samples from late gestation sows. Of the 16 samples, 8 were from sows at high risk and 8 from sows at low risk for POP. Of the 8 samples from sows at high risk for POP four subsequently experienced POP. Subsequent contigs were annotated to generate a gene catalog of the vaginal microbiome of sows. The contigs were binned into metagenome assembled genomes (MAGs), resulting in 10 high-quality MAGs identified as Mannheimia varigena, Corynebacterium maris, Turicibacter bilis, Staphylococcus hyicus, Streptococcus dysgalactiae, Anaerococcus prevotii, Actinobacillus rossii, Prevotellaceae, Methanobrevibacter, and Veillonella caviae. MAGs classified as Streptococcus dysgalactiae and Staphylococcus hyicus contained potential virulence factors that are linked to the weakening of the connective tissue of the reproductive tract. This work provides initial insights into the functional potential of the vaginal microbial communities in late gestation sows in relation to POP and reproductive health.