Production Systems and Age Influence Fecal Mycobiota Diversity and Composition in Swine.

The gut microbiome is an important factor in animal health and can be influenced by factors such as age, diet, stress, environmental conditions, and farming practices. Bacterial communities of the gut microbiome in many species have been extensively studied, but research on the fungal microbiota remains limited and underrepresented in the literature. The objective of this study was to characterize the fecal mycobiota of swine raised under two different production systems: outdoor pasture-based or conventional indoor systems. Fecal samples from nursery, growing-finishing, and sow pigs from both farming systems were collected, and the mycobiota was profiled using PCR amplification and sequencing of the universal fungal internal transcribed spacer 1 (ITS1) region. A significant difference in fungal community structure was observed between the conventionally raised and pasture-raised pigs, as well as among all three production phases. Four species, Arthrographis kalrae, Enterocarpus grenotii, Pseudallescheria angusta, and Sagenomella oligospora, were differentially abundant between the two farms, all of which had higher relative abundance in the pasture-raised pigs. Additionally, pasture-raised pigs hosted a more diverse fungal community with higher species richness in their gastrointestinal tract. In summary, farming practices and pig age influenced the pig fecal mycobiota.