Microbial diversity within the digestive tract contents of Dezhou donkeys

Gastrointestinal microbiota has significant impact on the nutrition and health of monogastric herbivores animals including donkey. However, so far the microbiota in different gastrointestinal compartments of healthy donkey has not been described. Therefore, we investigated the abundance and function of microbiota at different sites of the gastrointestinal tract (GIT) (foregut: stomach, duodenum, jejunum and ileum; hindgut: cecum, ventral colon, dorsal colon, and rectum) of healthy adult donkeys mainly based on 16S rRNA gene sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis. Collectively, our results showed that donkey has a rich, diverse and multi-functional microbiota along the GIT. In general, the richness and diversity of the microbiota are much higher in the hindgut relative to that in the foregut; at phylum level, the Firmicutes is dominant in the foregut while both Firmicutes and Bacteroides are abundant in the hindgut; at the genus level, Lactobacillus was dominant in the foregut while Streptococcus was more dominant in the hindgut. Our further PICRUSt analysis showed that varying microbiota along the GIT is functionally compatible with the corresponding physiological function of different GIT sites. For example, the microbes in the foregut are more active at carbohydrate metabolism, and in the hindgut are more active at amino acid metabolism. This work at the first time characterized the donkey digestive system from the aspects of microbial composition and function, provided an important basic data about donkey healthy gastrointestinal microbiota, which may be utilized to evaluate donkey health and also offer clues to further investigate donkey digestive system, nutrition, even to develop the microbial supplements.