Effect of diet on gut microbiota diversity in mandarin ducks (Aix galericulata) revealed by Illumina high-throughput sequencing.

The animal gut is a dynamic ecosystem. Many factors affect the structure and diversity of the gut microbiota, among which the composition of the diet is a direct determinant. To investigate the effect of dietary components on the gut microbiota of mandarin duck, nine fecal samples were collected from two foraging sites at Shiqian Mandarin Duck Lake National Wetland Park, Guizhou, China. We analyzed the chloroplast rbcL gene, mitochondrial COI gene, and 16S rRNA gene from the total DNA of the fecal samples by high-throughput sequencing to identify plant and animal components of the diet and the composition of the gut microbiota of mandarin duck. We found that the gut microbiota composition was significantly correlated with the number of species in the diet. Mandarin ducks with more diverse diets had a more complex gut microbiota with fewer pathogenic bacteria. This study provides further theoretical support for the effect of dietary differences on the structure of the host gut microbiota and clarifies the feeding preferences of mandarin duck in breeding areas.