Abstract：Rearing in cages is the development trend of duck production. This study analyzed the effects of rearing patterns on slaughter performance and intestinal microbiota in duck (Anas platyrhynchos). 16S rRNA high-throughput sequencing technology was used to reveal the fecal microbiota structure and composition in male and female ducks rearing on the floor or in cages groups. Forty ducks were selected from different rearing patterns. The slaughter performance was measured. Their fresh feces were collected from each duck. Total microbial DNA was extracted from feces samples. High-throughput sequencing was performed and the sequences were analyzed by QIIME 1.9.1 software. The results showed: 1) The slaughter performance of Gaoyou ducks was high. 2) The microbiota abundance and diversity of male ducks were higher than female ducks in rearing in cages group, but the abundance and diversity of fecal microbiota in female ducks were higher than male ducks in rearing on the floor group. The absolute dominant phyla in Gaoyou duck feces were Firmicutes and Bacteroidetes, the absolute dominant genera were Bacteroides and Romboutsia. Although there were no significant difference, the relative abundance values of dominant phylum and genera were different among groups. There were 6 species whose average relative abundance was more than 1%, such as Clostridiales bacterium, there were 50% species belonged to Bacteroides. 3) Compared to other groups, Bacteroides caecigallinarum was the differential microorganism in the feces of male duck in rearing in cages group, its relative abundance was significantly correlated with the pectoral muscle rate. Generally, rearing patterns and sex both affected fecal microbiota structure and composition in ducks, and the rearing patterns showed different effects on microbiota between sex, the abundance and diversity of male ducks rearing in cages was high. Bacteroides caecigallinarum may play an important role in the intestinal microbiota in ducks. The above results revealed that intestinal microbiota of ducks were affected by multiple factors, and regulation of intestinal microbiota could improve the production performance of duck.
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