Animal gut is a dynamic ecosystem, and there are many factors affecting the structure of intestinal flora and the diversity of intestinal microbes, among which food differences are the direct causes. To investigate the effect of food composition on the intestinal flora structure of mandarin duck during the reproductive period, 9 feces were collected from 2 foraging sites of 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 feces in detail to know the plants and animals in food compositions and intestinal bacteria of mandarin duck by high-throughput sequencing technology. We found that the gut microbiota composition were significantly correlated with the number of feeding species, the mandarin duck with a wide variety of feeding food had the more complex gut flora with more probiotics and less pathogenic bacterium. This study provides further theoretical support for food difference to affect the changes of intestinal bacterial structure of host, and provides scientific basis for understanding the feeding preference of mandarin duck at breeding area.

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Gut micriobiota have important roles in the immune, nutrition, and physiology of animals. To study the cause of gut microbiota change in black-necked cranes, we collected 9fresh Black-necked cranes’ fecal samples from Dashanbao Reserve. High throughput Illumina sequencing technology was used to analyze the microbial community structure of the collected samples for the V4 region of the 16S rRNA gene. Proteobacteria (44.14%) followed by Firmicutes (17.95%) and Bacteroidetes (9.97%) were the core dominant groups, and all of them play a role in the degradation of cellulose in Black-necked cranes. Bacteroidetes and Firmicutes contain glycan degrading enzymes, play a vital role in polysaccharide fermentation, and could help the host obtain more energy and materials. Higher Proteobacteria were unusual in birds. To explain this phenomenon, we analyzed the genus abundance of Proteobacteria in detail, found that Psychrobacter has the highest abundance and can grow at sub-zero temperatures. Through comparison, it was show that there were certain differences in the abundance of gut microbiota in different period The significance of this study was to provide a reference for understanding the function of intestinal microbiota and factors of gut microbiota structure change of Black-necked cranes and other migratory waterbirds.