PSLBI-6 Unveiling the gut mycobiota of pasture- and conventionally raised pigs

Abstract The gut microbiome has a significant role in mammalian health, in pigs it is influenced by factors such as age, diet, stress, environmental conditions, and farming practices. Although studies of the pig gut microbiome typically focus on bacteria, fungal members are understudied although they may have important roles in pig gut health. The objective of this research was to characterize the mycobiota in gastrointestinal tract of swine raised under two very different production systems, either outdoors on pasture or indoors in a farrow-to-finish operation (conventional). Fecal samples were collected from nursery (n = 7) and growing-finishing (n = 17) pigs as well as from sows (n = 11) on each of these conventional and pasture farms. After DNA extraction, the universal fungal internal transcribed spacer 1 (ITS1) region was PCR amplified and sequenced. A total of 353 fungal species spanning 234 genera and 6 phyla, were identified among all samples. Ascomycetes and Basidiomycetes were found to be the relatively most abundant phyla, comprising 96% of the mycobiota. There were 56 fungal species (relative abundance ≥ 0.10%) identified as differentially abundant in the fecal mycobiota of conventionally vs. pasture-raised pigs. Of these, 11 fungal species were relatively more abundant in the conventional pigs and 45 species were enriched in the pasture pigs. Kazachstania slooffiae, Penicillium polonicum, and Vishniacozyma victoriae were most strongly associated with the pigs raised under a conventional system while Enterocarpus grenotii, Leucosporidium escuderoi, and Sagenomella oligospora were among those species linked with pasture-raised pigs. Furthermore, E. grenotii was not detected in any of the conventionally raised pigs and K. slooffiae was not identified in the pigs raised on pasture. Pasture-raised pigs had significantly greater richness (number of amplicon sequence variants) and diversity (inverse Simpson diversity) in their fecal mycobiota compared with conventionally raised pigs (P < 0.05). Given these differences, it is therefore not surprising that the pigs raised under the two different systems had significantly different fungal community structures (R2 = 0.07, P < 0.001). Overall, the large differences observed between the two groups of pigs are a result of differences in diet, environment, and management system. In addition to their grain-based diet, pasture-raised pigs have access to plants and soil which may enrich their gut mycobiota as observed in the present study.