Microbial diversity within the digestive tract contents of Dezhou donkeys

Abstract

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.

Unveiling the Biogeography and Potential Functions of the Intestinal Digesta- and Mucosa-Associated Microbiome of Donkeys

“…This result suggests that the microbiota that colonized the mucosa originated from the digesta in the intestinal lumen. The dominant position of Lactobacillus at the genus level in the small intestine of the donkey was consistent with the results of a previous study (Liu et al, 2019). Lactobacillus was reported to have non-fibrous carbohydrate-degrading (e.g., pentoses, hexoses, and starch) capacity (Garrity, 2005), be involved the deconjugation of bile salts (Bao et al, 2012), and inhibit the proliferation of pathogenic bacteria by producing antimicrobial substances (such as bacteriocins and lactate) or competing with pathogenic bacteria for mucosal adhesion sites and nutrients (Savadogo et al, 2006;Umu et al, 2017).…”

“…However, limited information is currently available regarding donkey intestinal microbial composition and its potential metabolic impact. A few studies have focused on the fecal microbial composition of donkeys (Liu et al, 2014(Liu et al, , 2020, and a recent study has investigated the microbial composition and functions of digestive tract digesta in the Dezhou donkey (Liu et al, 2019). To our knowledge, no work has reported on the differences of digesta-and mucosa-associated microbiota in the different intestinal locations in the donkeys.…”

Morphophysiological Study of Gastrointestinal Tract of the Donkey (Equus asinus)

“…The donkey although is not more efficient in digestive process (grazing) compared to ruminants but has a combination of a large cecum and colon where the process of absorption and fermentation happens. Bacterial counts remain higher in equines where most of the fibrous and rough food digestion occurs [28]. The higher counts of hemicellulytic and cellulytic bacilli are present in the donkey cecum and in colon the luminal bacterial counts are even more.…”

The Composition and Predictive Function of the Fecal Microbiota Differ Between Young and Adult Donkeys

“…The bacterial primer pair 341F (5′-CCTAYGGGRBGC ASCAG-3′) and 806R (5′-GGACTACNNGGG TATCTAAT-3′) ( Sonnenburg et al, 2010 ) were used to amplify the V3–V4 regions of the bacterial 16S rRNA gene ( Liu et al, 2019 ) using Phusion High-Fidelity PCR Master Mix (NEB, New England Biolabs). Each primer contained the appropriate Illumina adapter sequence and 8-bp identifier indices.…”

“…Now, the Chinese livestock industry includes approximately 2,500,000 donkeys. In previous studies, we have examined the different digestive tract microbiota of donkeys ( Liu et al, 2019 ). However, limited information is known about the development of the bacterial community composition and function in the feces of donkeys at different ages.…”