The aim of this study was to investigate the difference of plasma biochemical parameters and intestinal microflora structure between different strains of Dezhou donkey (Sanfen donkeys and Wutou donkeys). Six healthy and nonpregnant Sanfen female donkeys and Wutou female donkeys aged 3 to 5 years and weighed 260 to 300 kg were randomly selected, the blood was collected from jugular vein, and the plasma biochemical parameters were determined by an automatic biochemical analyzer; the rectum content was aseptic collected, the high-throughput amplicon sequencing for 16S rDNA was performed using the Illumina MiSeq platform, and the bioinformatics analysis, correlation analysis and phenotypic prediction were performed on high-throughput sequencing data. The results showed as follows: 1) the total cholesterol (TC) content and alkaline phosphatase (ALP) activity in plasma of Sanfen donkeys were significantly higher than those of Wutou donkeys (P<0.05), and the triglyceride (TG) and total protein (TP) contents and aspartate transaminase (AST) and creatine kinase (CK) activities in plasma were significantly lower than those of Wutou donkeys (P <0.05). 2) The α diversity results showed that the ACE index, Chao index and Shannon index in rectal content microflora of Sanfen donkeys were significantly lower than those of Wutou donkeys (P<0.01); the β diversity results showed that the rectal content microflora overall structure was obviously segregated between Sanfen donkeys and Wutou donkeys, and the clustering degree of samples in the group was high. 3) There was no difference at the phyla level in rectal content microflora between Sanfen donkeys and Wutou donkeys, and Firmicutes and Bacteroidota were the dominant bacteria; at the genus level, the relative abundances of Lachnospiraceae_XPB1014 and Akkermansia in rectal content of Sanfen donkeys were significantly higher than those of Wutou donkeys (P<0.05), while the relative abundances of Prevotella and Phascolarctobacterium were significantly lower than those of Wutou donkeys (P<0.05). 4) The Spearman correlation analysis results showed that the Prevotella relative abundance was significantly positively associated with plasma AST activity and TG content (P<0.01), and was significantly negatively associated with plasma ALP activity and TC content (P<0.01); the Phascolarctobacterium relative abundance was significantly negatively associated with plasma TC content (P<0.05); the Akkermansia relative abundance was significantly positively associated with plasma ALP activity and TC content (P<0.01), and was significantly negatively associated with plasma AST activity and TG content (P<0.01); the Lachnospiraceae_XPB1014 relative abundance was significantly positively associated with plasma ALP activity and TC content (P<0.05 or P<0.01), and was significantly negatively associated with plasma AST activity (P<0.01). 5) The BugBase phenotypic prediction results showed that the potentially pathogenic of Sanfen donkeys was significantly lower than that of Wutou donkeys (P<0.05), and the contains mobile elements was significantly higher than that of Wutou donkeys (P<0.05). In conclusion, there are differences in the plasma biochemical parameters and the bacterial composition, relative abundance and function prediction in rectum between Sanfen donkeys and Wutou donkeys. From the perspective of plasma biochemical parameters and intestinal microflora structure, the Sanfen donkeys are better than the Wutou donkeys in terms of production performance and disease resistance.
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