Temporal dynamics of the fecal microbiome in female pigs from early life through estrus, parturition, and weaning of the first litter of piglets

Background: Age-associated changes in the gastrointestinal microbiome of young pigs have been robustly described; however, the temporal dynamics of the gut microbiome of the female pig from early life to first parity are not well understood. Our objective was to describe microbiome and antimicrobial resistance (AMR) dynamics of the fecal microbiome of breeding sows from early life through estrus, parturition and weaning of the first litter of piglets (i.e., from 3 to 53 weeks of age). Results Our analysis revealed that fecal bacterial populations in developing gilts undergo changes consistent with major maturation milestones. As the pigs progressed towards first estrus, the fecal bacteriome shifted from Rikenellaceae RC9 gut group- and UCG-002- dominated enterotypes to Treponema- and Clostridium sensu stricto 1 -dominated enterotypes. After first estrus, the fecal bacteriome stabilized, with minimal changes in enterotype transition and associated microbial diversity from estrus to parturition and subsequent weaning of first litter piglets. Unlike bacterial communities, fecal fungal communities exhibited low diversity with high inter- and intra-pig variability and an increased relative abundance of certain taxa at parturition, including Candida spp. Counts of resistant fecal bacteria also fluctuated over time, and were highest in early life and subsequently abated as the pigs progressed to adulthood. Conclusions The bacterial community and antimicrobial resistance of fecal bacteria in female pigs exhibited a stereotypic trajectory primarily driven by the physiological aging process. The fecal bacteriome enterotypes and diversity are found to be age-driven and established by the time of first estrus, with minimal changes observed during subsequent physiological stages, such as parturition and lactation, when compared to the earlier age-related shifts. Future analysis is needed to understand how our results compare to human microbiome dynamics, but the use of pigs as a model for humans is well-established and our findings suggest that the swine fecal microbiome matures in a stereotypic manner, which is a beneficial characteristic for an animal model system.