Development of the piglet fecal bacteriome and mycobiome from birth through weaning

The microbiota of the animal gastrointestinal tract is a critical component in host health, performance, and nutrition. Recently, the fungal microbiota (mycobiome) has been identified as a significant member of the microbiome. However, due to a limited number of cultureindependent studies on fungal microbiota in animal hosts, relatively little is known about the mycobiome in swine. In piglets, weaning is a period of stress, dietary changes, and a predisposition to infections, making it a time point of interest to industry. In this study, we characterized and compared the development of the bacteriome and the mycobiome in piglet feces from birth through the critical weaning transition (d 1–35 post-birth). Bacterial diversity increased over the experimental timeline, transitioning from an Enterobacteriaceae and Bacteroidaceae dominated population pre-wean (d 1–21) to fiber-degrading and short chain acid producing families Prevotellaceae and Ruminococcaceae post-wean (d 24–35). In comparison, fungal diversity peaked during the weaning transition (d 21–24) and decreased by d 35. The development of the mycobiome was characterized by an increased stable presence of dominant yeast families Debaryomycetaceae or Saccharomycetaceae post-wean (d 24–35) depending on litter. Based on mycobiome profiles of environmental sources, Saccharomycetaceae in the piglet gut likely originated from sow feces while Debaryomycetaceae may have originated from nursery feed. A co-occurrence network analysis of piglet feces from d 35 showed a strong association between fungal genera Kazachstania and Hyphopichia with the butyrate-producing and xylandegrading bacterial genus, Eubacterium rumantium, while Aspergillus demonstrated a negative association. This study provides insights into the early development and post-wean establishment of the fecal bacteriome and mycobiome in healthy piglets. Future studies will investigate the effect of the mycobiome on piglet growth and health during the weaning transition, including its role in fast- versus slow-growing piglets.

Key Words: pig, development, microbiome, mycobiome, bacteriome.

Presented at the Symposium on Gut Health in Production of Food Animals 2019 in St. Louis, USA.