Tracking the fecal mycobiome through the lifespan of production pigs and a comparison to the feral pig

Abstract

ABSTRACT Fungi in the pig gastrointestinal tract (the mycobiome) are believed to be important for host health and development. However, studies profiling the mycobiome over a production cycle and of the feral pig are lacking. The objectives of this study were to profile the pig mycobiome over one production cycle and profile the mycobiome of feral pigs. A total of 24 pigs from 12 litters ( n = 2 per litter) had fecal swabs taken at 11 days of age (D11), the day before weaning (W − 1), 7 days post-weaning (W + 7), and 119 days post-weaning (W + 119) in a research facility. Their dams ( n = 12) and an additional eight sows from a commercial barn had fecal swabs taken 3 days after farrowing. A total of 20 feral pigs had intestinal contents collected from the ileum and cecum for a total of 24 samples. Samples were analyzed via amplicon sequencing of the internal transcribed spacer 2 rRNA gene. Piglets tended to cluster based on their mother’s Kazachstania slooffiae levels on D11 ( P = 0.087) and significantly clustered on W + 119 ( P = 0.046). Piglets clustered with their littermate on D11 ( P = 0.006) and on W + 119 ( P = 0.007). In summary, we found that pigs maintain the same K. slooffiae status as their mothers until the end of the production cycle and show that the feral pig has a complex and unique mycobiome largely represented by ingested fungal species. IMPORTANCE This work provides evidence that early-life fungal community composition, or host genetics, influences long-term mycobiome composition. In addition, this work provides the first comparison of the feral pig mycobiome to the mycobiome of intensively raised pigs.