176 Characterizing the mycobiome in piglets during the weaning transition

Abstract

Abstract The importance of the microbiota in the gastrointestinal (GI) tract of animals is recognized as a critical player in host health. Recently, the significance of the mycobiome has been recognized, but culture-independent studies are limited, especially in swine. Weaning is a time of stress, dietary changes, and a predisposition to infections, making it a time of interest to industry. In this study, we sought to assess and characterize the mycobiome and microbiome in the feces and GI tract of swine from birth through the critical weaning transition (days 1–35 post-birth). In addition, we investigated environmental factors that may alter microorganisms present in piglets. Fecal bacterial populations increased in diversity over the experimental timeline and demonstrated a transition from an Enterobacteriaceae-dominated population, to a Prevotellaceae and Ruminococcaceae-dominated population by days 24–35 post-birth. These later populations are capable of fiber degradation and short chain fatty acid production. In fecal fungal populations, richness and diversity peaked at weaning and declined post-weaning. There was also a dynamic shift in the mycobiome to a Saccharomycetaceae-dominated population that remained stable into adulthood. Fungal organisms contributing to this colonization were not found in environmental samples including water, colostrum, and feed. Despite fungal populations present in the feces of sows, these maternal fungi were not similar to the piglet mycobiome and thus did not indicate a maternally-derived effect. Furthermore, the microbiomes of the GI tract showed decreased richness and diversity in the upper GI compared to the lower GI, and a high degree of individual variation and litter effect throughout the organs. This study provides insights into the early colonization and establishment of fungi during the weaning transition. Future studies will investigate the effect of the mycobiome on piglet growth and health during the weaning transition, including their role in fast- versus slow-growing piglets.