Abstract: Objective: The aim was to investigate whether a bacterial flora exists in the eggs of healthy laying ducks (Ma breed), and if yes, whether the bacterial flora could be associated with those in the genital tract and cecum. Methods: Healthy laying ducks were dissected to collect genital tract and cecum tissues, as well as soft- and hard-shelled duck eggs, and cultivable bacteria were counted by plate count method, and the diversity and correlation of uncultured bacterial flora were analyzed by MiSeq high-throughput sequencing. Results: The decreasing order of the total bacterial counts in the samples was cecum > genital tract > hard-shelled egg > soft-shelled egg. The bacterial gene sequences belonged to 56 phyla and 1 319 genera. The abundance and species evenness of bacteria in the cecum and genital tract were higher. The dominant genera included Bacteroides, Megamonas and Campylobacter. Species abundance and dominant concentration were higher in soft- and hard-shell eggs. Pseudomonas and Acinetobacter accounted for 19.01% and 10.01% of the total abundance, respectively. Gene function prediction showed that all samples had high abundance of metabolic and glycolytic functions. The gram-positive and anaerobic phenotypes in the cecum and genital tract were abundant. The pathogenicity and oxidative stress of bacteria in soft and hard shell eggs were significant. The dominant bacterial genera in the four samples were overlapped, and the overlap rates of egg content with the cecum and genital tract were 13.96% and 24.35%, respectively. In addition, the phylogenetic tree analysis showed that the genera in all samples were closely related to each other and shared homology with the significantly contributing genus Bacteroides in the cecum. Conclusion: Duck eggs are not formed in a sterile environment, the bacteria residing in the cecum and reproductive tract of healthy laying ducks can infect different egg structures during its formation and become a part of the internal flora in duck eggs. These results can provide a reference for further research on the characteristics and control of non-pathogenic bacteria in egg contents.

Key words: duck egg; cecum; reproductive tract; high-throughput sequencing; bacterial diversity