Abstract: To study the diversity and seasonal variation of bacteria contaminating duck eggshell surfaces, fresh duck eggs collected in different seasons were cleaned by ultrasonic washing to prepare bacterial samples. The diversity of bacterial flora in the samples was analyzed by Illumina MiSeq high-throughput sequencing. The results showed that a total of 697 244 optimal sequences were obtained and assigned to 650 operational taxonomic units (OTU), covering 35 phyla, 298 genera, and 447 species. For each seasonal samples, the dominant bacteria with a high relative abundance were Bacillus and Enterococcus (17.78% and 17.16%) of the phylum Firmicutes, and Escherichia-Shigella (17.14%) of Enterobacteriaceae in Proteobacteria. However, there was a significant difference in the microbial community structure and species richness among these samples. The maximum Chao and ACE were observed for winter samples (n = 4), with averages of 596.5 ± 22.29 and 587.5 ± 17.82, respectively, as well as maximum Shannon’s index and minimum Simpson’s index, 3.52 ± 1.02 and 0.1 ± 0.07 on average, respectively, indicating that the species complexity was highest. A total of 35 OTUs were common to the spring, summer, autumn and winter samples, accounting for 0.06%–70.00% of the total number of OTUs in each sample; and 9, 0, 17 and 496 OTUs were unique to these samples respectively. There were great differences in the composition of the microflora on the surface of eggshells among seasons. Vibrio, Pseudomonas_caeni, Enterobacter, Lysinibacillus, Clostridium_sensu_stricto_1 existed in different seasons. Some pathogenic floras were obviously affected by temperature. These results will provide a theoretical basis for further studies on the major spoilage bacteria of duck eggs and for controlling them.

Key words: duck eggshell; seasonal; high-throughput sequencing; bacterial diversity