Duck Eggs and Black-Yolked Salted Duck Eggs: Bacterial Diversity on Eggshells and Gene Function Prediction Using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt)

Abstract

After comparing the bacterial load of black-yolked salted duck eggs (BSE) and that of duck eggs with different cleanliness degrees, it was found that the total bacterial count on the shell of severely stained eggs (DE) was distinctly higher than that on the shell of non-visually stained eggs (CE), and the total bacterial count in the shell membrane and contents of BSE increased greatly. Furthermore, 16S rDNA gene sequencing was used to analyze the differences in the composition and abundance of bacterial communities in CE, DE and BSE. It turned out that Proteobacteria, Firmicutes and Actinobacteria were the dominant phyla, accounting for 34.35%, 27.25% and 17.28% of the total abundance, respectively, while Bacteroidetes accounted for 8.29% of the total abundance. Proteobacteria was the dominant bacteria in DE and accounted for 89.01% of the total abundance, while the relative abundance of Firmicutes and Actinobacteria were 6.16% and 3.98%. The dominant phyla in BSE were Proteobacteria (76.50%), Bacteroidetes (8.00%), Actinobacteria (6.76%) and Firmicutes (5.43%). The abundance of Proteobacteria in DE and BSE was significantly increased. The dominant bacterial genera in CE were Nesterdella (9.08%), Campylobacter (7.91%), Streptococcus (3.41%) and Oligomonas (2.92%). In DE, Psychrobacter was the dominant genus, accounting for 86.01% of the total abundance, and the relative abundance of Acinetobacter was 2.20%. The dominant bacteria in BSE were Rolstonia (22.91%), Serratia (5.05%) and Actinomycetes (3.32%). The cluster analysis of bacterial diversity showed that the dominant microorganisms of BSE were close to those of DE. The microbial phenotype analysis showed that the dominant microorganisms of BSE were Gram-negative bacteria, had high oxidative stress tolerance and pathogenicity, and could tolerate oxidizing detergents. The results of microbial gene function prediction and species composition of metabolic pathways demonstrated that bacterial carbohydrate decomposition, lipid transport and metabolic oxidation in DE were stronger than those in CE. More coenzyme transport and metabolic pathways could make the biochemical reactions of bacteria from DE faster to produce more secondary metabolites, thus resulting in changes in the quality of duck eggs. This is consistent with the highest bacterial abundance in the secondary metabolite biosynthesis, transport and catabolism pathways in BSE. The results of this study provide theoretical support for the cleaner production of duck eggs.

Keywords

• duck eggs; high-throughput sequencing; bacterial diversity; function prediction