Bacterial Community Structures in Raw Pork from Supermarkets and Farmers’ Markets Determined by High-Throughput Sequencing Analysis

Pork contaminated with bacteria can shorten the shelf life and cause foodborne diseases. Bacterial community analysis of raw pork in sale process can help identify bacteria associated with food quality and safety. In this study, 52 pork samples were collected from various supermarkets and farmers' markets in Qingdao, China. And the bacterial community structures in pork were analyzed by high-throughput sequencing of 16S rDNA. Both the <i>α</i>-diversity and <i>β</i>-diversity of bacterial communities in pork samples from farmers' market were higher than those from supermarkets (ANOSIM test, <i>R</i>² = 0.049, <i>p</i> = 0.016). <i>Proteobacteria</i> (88.8%) was the most dominant phylum, and <i>Photobacterium</i> (44.5%) and <i>Acinetobacter</i> (23.9%) were the top two dominant genera in all pork samples. The abundance of most dominant bacterial genera was higher in pork samples from farmers' markets than those from supermarkets, But <i>Photobacterium</i> (ranking first) was just the opposite (<i>p</i> = 0.003). The bacterial communities in pork hadn't obvious clustering characteristics between the two sale locations, while <i>Photobacterium</i> was considered as the biomarker in pork samples from supermarkets according to LefSe analysis (linear discriminant analysis score >4.0). A strong correlation was observed between some samples (R >0.7) collected from different stalls within the same sampling location, indicating cross-contamination possibility in sale process. The findings may have implications for the quality and safety control of pork, particularly for microbial prevention and control during selling and consumption.