Pork is widely consumed globally, and pigs' microbiota can potentially harbor foodborne pathogens. Contaminated pork in retail markets poses significant implications for food quality and safety. However, limited studies have compared pork microbiomes in various marketing environments. In this study, we utilized traditional microbial culture methods and high-throughput 16S rRNA sequencing to assess pathogen contamination and bacterial diversity in raw pork samples purchased from farmers' markets and two types of supermarkets (upscale and ordinary) in Hangzhou, China. Traditional microbial plate cultures identified E. coli and Salmonella spp. in 32.1% (27/84) and 15.5% (13/84) of the collected pork samples, respectively. Moreover, 12 out of 13 Salmonella strains were found in farmers' markets. The MIC results indicated a high prevalence of MDR strains, accounting for 51.9% in E. coli and 53.8% in Salmonella. The prevalence of NaClO tolerant strains was 33.3% and 92.3% for E. coli and Salmonella, respectively. Sequencing results indicated significantly higher microbial diversity in farmers' market samples compared to supermarket samples. Farmers' market pork samples exhibited a greater abundance of Acinetobacter, while Pseudomonas and Brochothrix were predominant in supermarket samples. The total abundance of pathogenic and spoilage bacteria was also higher for the farmers' market samples. Cross-contamination during market trading was evident through a high correlation between bacterial abundance in pork from different stalls within the same farmers' market. PICRUSt2 analysis identified significant differences in the average proportions of genes for carbohydrate, energy, and lipid metabolism from the farmers' markets, suggesting an exacerbation of microbial metabolic activity and increased perishability of pork in this environment. In conclusion, this study revealed variations in the characteristics of raw pork bacterial contamination across different types of retail stores, as well as differences in the composition and diversity of their respective bacterial communities.
Keywords: bacterial community; bacterial contamination; high-throughput sequencing; pork; retail markets.