The Fungus Among Us: Exploring the Porcine Mycobiome
Creators: Prisnee, Tausha L
Publisher: name: University of Alberta Library
Year: 2023

<p>Microbes in the intestinal tract are essential for host health and development. While the role of bacteria in these process is well studied, the role of fungi (the mycobiota) have received less attention. However, fungi have been shown to alter immune system development and intestinal architecture. The objectives of this thesis were to explore the impact of antibiotic treatment on fungal community structure, to track and profile the pig mycobiome over 1 production cycle with comparisons to commercially raised and feral pigs, and to determine the impact of Kazachstania slooffiae on bacterial community structure, metabolite production, intestinal and immune system development. <br>
In study 1, 32 piglets from 4 different litters were randomly assigned to one of 4 treatment groups: placebo (P) amoxicillin (A) amoxicillin + clavulanic acid (AC) or gentamicin + ampicillin (GA). Bacterial and fungal community structure were investigated by sequencing the 16S rRNA gene and the internal transcribed spacer-2 (ITS2) rRNA gene, respectively. Total bacteria and total fungi were quantified by quantitative polymerase chain reaction. This study showed that antibiotics did not alter fungal community composition (P = 0.834), however, AC treatment increased the ratio of total fungi to total bacteria (P = 0.027). Additionally, the maternal mycobiome drove piglet mycobiome composition, especially with regard to the yeast K. slooffiae. We found that piglets were more similar to their maternal sow than to any of the other sows in the study (P  ≤  0.05). <br>
In study 2, 2 piglets from 12 different litters were fecal sampled at 11 days of age, the day before weaning, 7 days after weaning and 119 days after weaning. Additionally, 8 sows in a commercial facility and feral pigs were sampled. Fungal community structure was evaluated via sequencing of the ITS2 rRNA gene. We found that piglets clustered by sow  K. slooffiae status at 11 days of age (P = 0.087) and 119 days after weaning (P = 0.046), but not on the day before (P = 0.297) or 7 days after weaning (P = 0.859). Piglets were more similar to their maternal sow than a random sow at 11 days of age (P  &lt; 0.001) but not after (P ≥ 0.05). Additionally piglets clustered with their litter mate at 11 days of age (P = 0.006) and 119 days after weaning (P = 0.007), but not on the day before weaning (P = 0.184) or 1 week after weaning (P = 0.087). Together these results suggests that what piglets are exposed to in the farrowing pen can have long-term impacts on mycobiome composition. Commercial sows were found to be variable in the amount of K. slooffiae present. Feral pigs had a more complex mycobiome consisting predominantly of fungi associated with soil.<br>
In study 3 we used a gnotobiotic piglet model to study the impact of K. slooffiae on bacterial community structure, metabolite production, and immune system and intestinal development. We found that K. sloofffiae altered the bacterial community and increased the amount of total bacteria present in the intestine (P ≤ 0.05). K. slooffiae colonization altered the ileal metabolome including increasing butyrate levels (P = 0.032). K. slooffie also resulted in a greater villus height to crypt depth ratio in the ileum (P = 0.028) suggesting increased absorptive capacity and the immune system was altered both in terms of cytokine production and immune cell phenotype (P  ≤ 0.05).<br><br>
In summary, this thesis shows that shaping early life fungal exposure may have long-term impacts on mycobiota composition, and that K. slooffiae is an active member of the core pig mycobiota that may play a role in pig health. </p>