Structural and functional characteristics of faecal, vaginal and colostrum microbiota in high-yielding sows

Recent studies have highlighted the critical roles of the microbiota in faeces, vagina and colostrum in reproductive success and piglet development. Understanding the structural and functional dynamics of these microbial communities is essential for optimizing the health and productivity of high-yielding (HY) sows. This study aimed to characterize the structural and functional features of these microbial communities in HY sows (litter size>10 piglets) vs. low-yielding (LY) sows (≤10 piglets) and to explore their associations with sow performance and piglet health. Fifteen Yorkshire sows from each group were selected, and fresh faecal, vaginal mucus and colostrum samples were collected post-parturition. Microbial composition was analysed using 16S rRNA gene amplicon sequencing, and functional potential was predicted via PICRUSt2. Results showed that HY sows exhibited higher alpha diversity in vaginal and colostrum microbiota and greater community stability (higher neutral community model <i>R</i> ² values) compared to LY sows. In faeces, HY sows were enriched with <i>Terrisporobacter</i> and <i>Romboutsia</i>, while depleted in <i>Ruminococcus</i>_<i>torques</i>_group. In the vagina, <i>Campylobacter</i> and <i>Peptoniphilus</i> were increased, whereas <i>Eubacterium</i>_<i>nodatum</i>_group decreased. In colostrum, <i>Lactobacillus</i>, <i>Bifidobacterium</i> and <i>Romboutsia</i> were enriched, with reduced <i>Peptostreptococcus</i>, indicating a more beneficial profile for neonatal health. Functional predictions revealed distinct metabolic profiles: HY faecal microbiota upregulated cysteine/methionine metabolism and porphyrin and chlorophyll metabolism; vaginal microbiota enhanced oxidative phosphorylation and thiamine metabolism; colostrum microbiota showed enrichment in monobactam and novobiocin biosynthesis, which is associated with antimicrobial activity and stress response. These findings demonstrate that HY sows harbour a more stable and functionally advantageous microbiome across multiple biological niches, which may contribute to superior reproductive performance and improved offspring health. The results provide a foundation for developing microbiome-targeted strategies to enhance productivity and welfare in commercial pig production.