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.

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 (GI) 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 GI tract organs and feces from 35-day old piglets. Following weaning, the α-diversity and amplicon sequence variants (ASVs) counts of the bacteriome increased, proximally to distally, from the stomach to the feces along the GI tract, while the mycobiome α-diversity and ASV counts were highest in the porcine stomach. β-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 GI tract and feces of piglets directly following weaning and the potential interactions of these microbes in the porcine gut ecosystem.

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 (days 1 to 35 postbirth), 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 because of the dominance of Kazachstania slooffiae, a poorly characterized colonizer of animal gastrointestinal 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.