Abstract: Next generation sequencing (NGS) is a new sequencing method invented at the beginning of the 21st century on the basis of first-generation sequencing technology. With its high throughput, high accuracy and abundant genetic data, NGS has been gradually applied to the dairy industry and has played an important role in ensuring the quality and safety of dairy products. On the one hand, this paper introduces the application of whole genome sequencing (WGS) technology to identify contaminated microorganisms, pathogen traceability, strain polymorphism, antibiotic resistance and virulence factor carrying status analysis. On the other hand, this paper focuses on the application of metagenomic sequencing technology in research on the application of microbial diversity, including microbial diversity investigation in the processing environment of dairy products, environmental microorganism monitoring of dairy factories, shelf-life assessment of dairy products, microbial risk monitoring of raw materials, and authenticity assessment of dairy products. Finally, this paper comprehensively analyzes and discusses the challenges and future prospects for the application of NGS technology in the field of dairy products.

Key words: next generation sequencing; whole genome sequencing; metagenomics; quality and safety of dairy products

摘要： 下一代测序（next generation sequencing，NGS）技术是在一代测序技术基础上于21世纪初发展起来的一种高通量测序方法。NGS具备高通量、高准确度和丰富的遗传数据信息量，因此逐步应用于乳制品工业领域，在确保乳品质量与安全方面发挥重要作用。本文一方面介绍利用全基因组测序技术进行污染微生物鉴定、致病菌溯源以及菌株多态性、病原菌耐药性与毒力因子携带状况分析等；另一方面重点介绍基于宏基因组测序技术开展乳制品加工环境微生物多样性调查、工厂环境微生物监控、货架期评估、原料微生物风险监控及食品真实性评估等菌群多样性相关应用研究。最后，本文针对NGS技术在乳制品领域实际应用过程中面临的挑战和应用前景进行全面分析与讨论。

关键词: 下一代测序；全基因组测序；宏基因组；乳制品质量与安全