The piglet mycobiome during the weaning transition: a pilot study

Authors: Summers, Katie; Foster Frey, Juli; Ramsay, Timothy; ARFKEN, ANN - US Department Of Agriculture (USDA)

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/17/2019
Publication Date: 5/28/2019
Citation: Summers, K.L., Foster Frey, J.A., Ramsay, T.G., Arfken, A.M. 2019. The piglet mycobiome during the weaning transition: a ailot study. Journal of Animal Science. https://doi.org/10.1093/jas/skz182.
DOI: https://doi.org/10.1093/jas/skz182

Interpretive Summary: The weaning transition is a stressful event in a piglet's life and can lead to poor growth performance and changes in the microbiome and mycobiome. These changes are poorly understood but can lead to post-weaning diarrhea and potential susceptibility to other diseases, resulting in significant financial loss to farmers. Antibiotics have been used in swine production to promote growth and combat post-weaning diarrhea, but the recent banning of antibiotics for growth promotion has made understanding the microbiome and the mycobiome of piglets even more critical in understanding piglet health during weaning and to create potential interventions in poor-performing piglets. Scientists at the Agricultural Research Service, Beltsville, Maryland analyzed the microbiome and mycobiome in piglets from birth through two weeks post-weaning. USDA scientists demonstrated the ability to isolate fungal DNA and sequence with high throughput sequencing technology to analyze difficult mycobiome populations. Fecal samples collected for 5 weeks demonstrated that the mycobiome and microbiome go through substantial and consistent shifts in populations at the point of weaning, including the introduction and dominance of the fungus, Kazachstania slooffiae. This pilot study provides insights into the microbial populations in piglets during weaning and future studies will investigate the effect of these populations on piglet growth performance and health.

Technical Abstract: The importance of the microbiota in the gastrointestinal tract of animals is recognized as a critical player in host health. Recently, the significance of the mycobiome has been recognized, but culture-independent studies are limited, especially in swine. Weaning is a time of stress, dietary changes, and a predisposition to infections, making it a time point of interest to industry. In this pilot study, we sought to assess and characterize the mycobiome in the feces of swine from birth through the critical weaning transition to investigate the mycobiome population and its temporal dynamics in piglet feces. Cultured fecal samples demonstrate a significant increase in fungal burden following weaning, that does not differ from adult levels, suggesting stable colonization. Culturable fungi were not found in any environmental samples tested, including water, food, sow milk or colostrum. To determine the fungal diversity present and to address the problem of unculturable fungi, we performed a pilot study utilizing ITS and 16S rRNA focused primers for high throughput sequencing of fungal and bacterial species, respectively. Bacterial populations increase in diversity over the experimental timeline (d 1-35 post-birth) but the fungal populations do not demonstrate the same temporal trend. Following weaning, there is a dynamic shift in the feces to a Saccharomycetaceae-dominated population. The shift in fungal population was due to the dominance of Kazachstania slooffiae, a poorly characterized colonizer of animal GI tracts. This study provides insights into the early colonization and subsequent establishment of fungi during the weaning transition in piglets. Future studies will investigate the effect of the mycobiome on piglet growth and health during the weaning transition.