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.
Highlights
The gastrointestinal (GI) tract is home to the gut microbiome, trillions of colonizing and transient microbes
While many studies have focused on the bacterial component of the microbiome, the bacteriome, recent studies have demonstrated the ability of fungal microbiome members, the mycobiome, to alter gut microbial community structure and cause disease [1,2,3,4,5]
The bacteriome transitioned from a Proteobacteria- to a Firmicutes- and Bacteroidetes-driven community (Figure S4A)
Summary
The gastrointestinal (GI) tract is home to the gut microbiome, trillions of colonizing and transient microbes These microbes support critical health functions including digestion, immune development, metabolism, and resistance to pathogens. The weaning transition involves drastic changes in diet and environment, resulting in stress and broad alterations in the microbiome These changes can result in poor growth performance and a predisposition to infections, such as post-weaning diarrhea, making potential health interventions of interest to industry and farmers [10,11,12]. Previous work from our laboratory investigated the bacterial and fungal members of the piglet mucosal-associated gastrointestinal tract microbiome two weeks post-weaning (day 35) to characterize the healthy microbiome. The aim of this study was to analyze the temporal development of both the fecal microbiome and mycobiome from birth through two weeks post-weaning in healthy piglets to help gain insight into potential dietary interventions during this critical period
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