Identification of core microbiotas in European sows during gestation and lactation: links to performance

Background The gut microbiota is a critical factor influencing the health and productivity of sows, with implications for sustainable swine production. This study aimed to identify key factors shaping the sow gut microbiota across six European countries and characterize the composition of the core gut microbiota during late gestation and lactation. Results We identified two distinct sow gut core microbiotas at gestation and lactation shared across the six examined European countries comprising ~ 50% of the relative abundance at both timepoints. Of the 40 most abundant species, only 21 overlapped between late gestation and lactation, demonstrating significant shifts in microbial composition. Streptococcus suis was more abundant during gestation, while multiple Clostridium and Terrisporobacter species dominated during lactation. Country-specific differences in microbial composition were observed, with Spanish farms showing high abundances of Escherichia coli and Streptococcus alactolyticus , while Danish farms exhibited unique species such as Romboutsia timonensis . The time in the reproductive cycle was the most influential factor on the microbial composition, outweighing country, feed and parity. Importantly, the gut microbiota composition was linked to sow performance. Low-performing sows displayed a failure to transition from the gestation-associated microbiota to a distinct lactation-associated microbiota, as evidenced by species such as Streptococcus suis remaining elevated into lactation. Differential abundance analyses identified six species including E. coli and S. suis being associated with low performance, highlighting the importance of microbial maturation during the reproductive cycle. Conclusion This study underscores the importance of the reproductive stage in shaping the sow gut microbiota with distinct gestation and lactation core microbiotas shared across countries and linked to performance, providing insights for improving sow health and productivity.