Spatial variations in the microbiota: comparative analysis of microbial composition and predicted functions across different intestinal segments and feces in donkeys

Donkeys, as single-stomach herbivores, have a complex and diverse microbial community in their digestive tracts. The intestinal bacterial community is crucial for maintaining intestinal homeostasis, as well as the host’s overall nutrition and health. However, research on donkey gut microbes is relatively limited, particularly regarding the microbial colonization patterns in different intestinal segments of adult donkeys. Therefore, this study examined the abundance and function of microbiota across various sites of the intestinal tract (duodenum, jejunum, ileum, cecum, colon) and feces of healthy adult Dezhou male donkeys using 16S rRNA gene sequencing and PICRUSt analysis. The results indicate that donkeys have a rich gut microbial diversity and a large microbial population. No significant differences in the indices of alpha diversity were observed among the donkey’s duodenum, jejunum, ileum, cecum, colon, and feces. A Venn diagram analysis revealed the presence of both unique (Duodenum: 4645; Jejunum: 3586; Ileum: 4904; Cecum: 4253; Colon: 6135; Feces: 4885) and shared (339) ASVs among the different sections. A principal coordinate analysis (PCoA) revealed significant differences (R2 = 0.2076, p