Impact of weaning on piglet microbiota: differences in bacterial taxa and metabolic pathways associated with diarrhea

In modern pig farming, early weaning increases pigs' vulnerability to intestinal diseases due to the immaturity of their digestive and immune systems. Post-weaning diarrhea is a common issue in Brazil, leading to weight loss and slow growth, which significantly impacts the swine industry's performance. The intestinal microbiota plays a crucial role during this phase, as it is determinant for the animals' health and productivity. This study aimed to compare the microbiota of post-weaning piglets with and without diarrhea, identifying differences in the bacterial composition and microbial metabolic pathways. The most frequent phyla in both groups were Bacillota followed by Bacteriodota and Pseudomonadota, which together accounted for nearly 90% of microbiota. However, one phylum and eight bacterial families were enriched in the control group (minimum fold change of 4.6), whereas only the Fusobacteriaceae family was enriched in diarrhea group (fold change of 6.5). Moreover, 16 genera were enriched in the control group, while 12 were enriched in the diarrhea group. These findings indicate distinct microbiota compositions between the groups, suggesting an association with dysbiosis. Variations in metabolic pathways were also observed. In the diarrhea group, six pathways were enriched (fold changes of 8.12-263.23), most of which were associated with pathogenic and inflammatory processes. In addition, an increase in pathways linked to bacterial metabolism suggested heightened microbial activity, potentially exacerbating diarrhea. In contrast, seven metabolic pathways were enriched in the control group, many of which are essential for immune system development and strengthening, supporting healthy growth. These results highlight key differences in the microbiota and metabolic activity of piglets with and without diarrhea, providing insights that may aid in developing strategies to promote intestinal health and improve post-weaning performance.