Microbiota Profiles of Hen Eggs from the Different Seasons and Different Sectors of Shanghai, China

Hen eggs are one of the most popular foods worldwide, and their safety is critical. Employing 16S rRNA full-length sequencing is an effective way to identify microorganisms on or in eggs. Here, hen eggs collected from poultry farms over four seasons, as well as from markets in Shanghai, were analyzed with third-generation sequencing. Firmicutes (44.46%) and Proteobacteria (35.78%) were the two dominant phyla, and Staphylococcus, Acinetobacter, Aerococcus, Psychrobacter, and Lactobacillus were the dominant genera. The dominant genera on the eggshell surfaces from the farms varied with the seasons, and the highest contamination of Staphylococcus (32.93%) was seen in the eggs collected during the summer. For the market samples, Pseudomonas was the most abundant in content, with Staphylococcus being the most-often genera found on the eggshell surfaces. Moreover, several potential pathogenic bacteria including Riemerella anatipestifer (species), Klebsiella (genus), and Escherichia/shigella (genus) were detected in the samples. The results revealed the impacts of weather on the microbiota deposited on an eggshell’s surface, as well as the impacts due to the differences between the contents and the surface. The results can help disinfect eggs and guide antibiotic selection.