Temporal dynamics of the gut bacteriome and mycobiome in the weanling pig

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

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/4/2020
Publication Date: 6/9/2020
Citation: Arfken, A.M., Foster Frey, J.A., Summers, K.L. 2020. Temporal dynamics of the gut bacteriome and mycobiome in the weanling pig. Microorganisms. https://doi.org/10.3390/microorganisms8060868.
DOI: https://doi.org/10.3390/microorganisms8060868

Interpretive Summary: The environmental changes and stress associated with the weaning transition in piglets can lead to poor growth performance and a predisposition to disease. Interactions between the bacteriome and mycobiome can result in altered host nutrition, development, and disease response, but these interactions remain poorly understood in swine. Scientists at the Agricultural Research Service, Beltsville, Maryland analyzed the bacteriome and mycobiome in the feces of piglets from birth through 2 weeks post-weaning (35 days of age). USDA scientists demonstrated that the interactions between bacterial and fungal populations are changed by piglet development. The bacteriome had a predictable pattern of colonization with increased diversity over time while the mycobiome demonstrated reduced diversity over time. Further, fungal populations were more effected by environmental effects such as feed, showing them to be a more transient population than the bacteriome. These data together suggest that the mycobiome may be an effective target for microbial interventions due to its tractability and ability to alter the bacteriome during the weaning transition in piglets. This data provides insights into microbial interactions in the piglet fecal ecosystem during weaning and future studies will investigate its role in piglet growth performance.

Technical Abstract: Weaning is a period of environmental changes and stress that results in significant alterations to the piglet gut microbiome and is associated with a predisposition to disease, making potential interventions of interest to the swine industry. In other animals, interactions between the bacteriome and mycobiome can result in altered nutrient absorption and susceptibility to disease, but these interactions remain poorly understood in pigs. Recently we assessed the colonization dynamics of fungi and bacteria in the gastrointestinal tract of piglets at a single time point post-weaning (day 35) and inferred interactions were found between fungal and bacterial members of the porcine gut ecosystem. In this study, we performed a longitudinal assessment of the fecal bacteriome and mycobiome of piglets from birth through the weaning transition. Piglet feces in this study showed a dramatic shift over time in the bacterial and fungal communities, as well as an increase in network connectivity between the two kingdoms. The piglet fecal bacteriome showed a relatively stable and predictable pattern of development from Bacteroidaceae to Prevotellaceae, as seen in other studies, while the mycobiome demonstrated a loss in diversity over time with a post-weaning population dominated by Saccharomycetaceae. The mycobiome demonstrated a more transient community that is likely driven by factors such as diet or environmental exposure rather than an organized pattern of colonization and succession evidenced by fecal sample taxonomic clustering with nursey feed samples post-weaning. Due to the potential tractability of the community, the mycobiome may be a viable Candidate for potential microbial interventions that will alter piglet health and growth during the weaning transition.