The metagenomic dataset of meat and its surrounding environment from three markets in Xiamen.

Meat products (including chicken, marinated chicken, pork, and marinated pork) and environmental samples were collected in triplicate from produce markets located in Xiamen. These samples were kept on ice and then transported immediately to the laboratory, which were stored at -20℃ before DNA extraction. DNA was extracted from meat and environmental samples using the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, USA) according to the manufacturer’s guidelines. Followed by metagenomic analysis. In 2021, samples of raw chicken, raw pork, marinated chicken, marinated pork, and the surrounding environment were collected from market in Jimei District. In 2025, samples of marinated pork and the surrounding environment were obtained from markets in Haicang and Tong'an Districts.