Product-specific microbial community dynamics in egg-based processed foods: Integrated analysis of processing facility environments and retail products.

Egg-based processed foods are widely consumed under refrigerated or frozen conditions; however, microbial community dynamics across products and processing environments remain poorly characterized. Here, we integrated culture-dependent enumeration and 16S rRNA gene sequencing to characterize microbial communities in commercially distributed egg garnish (n = 61) and rolled egg products (n = 109), as well as stage-resolved samples from a processing facility (n = 99). Both production lines originated from a common liquid whole egg input but diverged at the genus level along their respective processing trajectories. Thermal processing reshaped microbial communities, while processing environments influenced final product composition; sequencing additionally revealed taxa missed by culture-dependent enumeration, including Vibrio. SourceTracker analysis revealed distinct contamination pathways: post-thermal environments such as heating-room floors and worker gloves contributed substantially to egg garnish microbiota, whereas early-stage inputs such as liquid whole egg and vegetable wash areas were the primary sources for rolled egg products. At retail, microbial communities differed significantly between product types. Egg garnish was dominated by environmental and psychrotrophic genera such as Pseudomonas, suggesting cold-storage spoilage risk, whereas rolled egg products were enriched in lactic acid bacteria such as Lactococcus. Acinetobacter and lactic acid bacteria detected in final processing-facility products were also recovered from retail samples, indicating potential transmission across the production chain. Overall, microbial community structure is shaped by product formulation and processing conditions, highlighting product-specific spoilage and safety management strategies.