Microbiota of eggs revealed by 16S rRNA-based sequencing: From raw materials produced by different suppliers to chilled pasteurized liquid products

In this study, the microbiota of liquid eggs (raw materials) produced by different suppliers and final products (chilled pasteurized liquid whole eggs and chilled pasteurized liquid egg yolk) (n = 211, pooled in 21 samples) was studied by a 16S rRNA-based amplicon sequencing. The raw material samples were collected from five different egg suppliers (A, B, C, E, and F), whereas the sixth type of raw material was whole shell eggs broken at the egg processing factory. The suppliers were located at different distances (∼100 Km to ∼1500 Km) from the liquid egg processing facility, being subjected to varying practices after egg breaking (pasteurization and addition of hydrogen peroxide), followed by chilled transportation. The results showed that final products presented lower diversity indexes than raw materials suggesting that processing and storage act towards shaping their microbiota. Besides, the transportation distance seemed to influence the microbiota of liquid egg. Proteobacteria and Firmicutes dominated the sequences of 16S rRNA in raw materials and final product samples, while the abundance of classes was found to vary considerably among samples and composite samples. Lactobacillales and Pseudomonadales were the most abundant order in almost all raw material samples, whereas Enterobacteriales was abundant in few raw material samples. The principal genera linked to final products were Pseudomonas, Carnobacterium and less frequently Clostridium. The study highlights that the practices employed by suppliers and transportation distances are key in modulating the microbiota of raw materials and further liquid processed egg products.