Yeasts of burden: exploring the mycobiome-bacteriome of the piglet GI tract

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

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/19/2019
Publication Date: 10/8/2019
Citation: Arfkin, A.M., Foster Frey, J.A., Ramsay, T.G., Summers, K.L. 2019. Yeasts of burden: exploring the mycobiome-bacteriome of the piglet GI tract. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2019.02286.
DOI: https://doi.org/10.3389/fmicb.2019.02286

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 bacteriome and mycobiome. The interactions between the bacteriome and mycobiome in the piglet gut remain unknown but can result in altered nutrition, pathogenicity of infection, and host development, making them a crucial component in host health. 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. Scientists at the Agricultural Research Service, Beltsville, Maryland analyzed the bacteriome and mycobiome in the feces and gastrointestinal (GI) organs of post-weaning piglets (35 days of age). USDA scientists demonstrated the distinct differences in bacterial and fungal diversity and colonization of the GI tract and feces of piglets. Further, while humans are normally colonized by Candida spp., piglets were found to be colonized by a distinct, yet related fungus, Kazachstania spp. Lastly, potential interactions were found in the lower piglet GI bacteriome and mycobiome with positive correlations found between the fungus, Kazachstania, and several bacterial species, including Lactobacillus. Aspergillus demonstrated negative correlations with the short chain fatty acid-producing bacteria Butyricoccus, Subdoligranulum, and Fusicatenibacter. This study is the first to provide a detailed analysis of the mycobiome in post-weaning piglets and provides insights into the microbial interactions in the piglet gut ecosystem following weaning. Future studies will investigate the effect of these populations on piglet growth performance and health.

Technical Abstract: Interactions between the bacteria and fungi in the gut microbiome can result in altered nutrition, pathogenicity of infection, and host development, making them a crucial component in host health. Associations between the mycobiome and bacteriome in the piglet gut, in the context of weaning, remain unknown. Weaning is a time of significant stress, dietary changes, microbial alterations, and a predisposition to infection. The loss of animal health and growth makes potential microbial interventions of interest to the swine industry. Recent studies have demonstrated the diversity and development of the microbiome in the gastrointestinal tract of piglets during weaning, resulting from the dietary and physiological changes. Despite these advances, the role of the mycobiota in piglet health and its contribution to overall microbiome development remains mostly unknown. In this study we investigated the bacteriome and the mycobiome after weaning in the gastrointestinal tract organs and feces from 35-day old piglets. Following weaning, the a-diversity and amplicon sequence variants (ASV) counts of the bacteriome increased, proximally to distally, from the stomach to the feces along the GI tract, while the mycobiome a-diversity and ASV counts were highest in the porcine stomach. ß-diversity analyses show distinct clusters based on organ type in the bacteriome and mycobiome, but dispersion remained relatively constant in the mycobiome between organ/fecal sites. Bacteroidetes, Firmicutes, and Epsilonbacteraeota were the most abundant bacterial phyla present in the GI tract and feces based on mean taxonomic composition with high variation of composition found in the stomach. In the mycobiome, the dominant phyla were Ascomycota and Basidiomycota, and the stomach mycobiome did not demonstrate the same high level of variation observed in the bacteriome. Potential interactions between genera were found in the lower piglet GI bacteriome and mycobiome with positive correlations found between the fungus, Kazachstania, and several bacterial species, including Lactobacillus. Aspergillus demonstrated negative correlations with the short chain fatty acid-producing bacteria Butyricoccus, Subdoligranulum, and Fusicatenibacter. This study demonstrates the distinct colonization dynamics between fungi and bacteria in the gastrointestinal tract and feces of piglets directly following weaning and the potential interactions of these microbes in the porcine gut ecosystem.