Yang Qiuping, Wang Xiaoqi, Han Mengting, Sheng Huanjing, Sun Yulu, Su Li, Lu Wenjing, Li Mei, Wang Siyue, Chen Jia, Cui Shenghui, Yang Bao-Wei
College of Food Science and Engineering, Northwest A&F University, Shaanxi, China.
College of Chemical Technology, Shijiazhuang University, Shijiazhuang, China.
Appl Environ Microbiol. 2025 Jun 18;91(6):e0251224. doi: 10.1128/aem.02512-24. Epub 2025 May 16.
With the continuous advancements in high-throughput genome sequencing technologies and the development of innovative bioinformatics tools, bacterial genome-wide association studies (BGWAS) have emerged as a transformative approach for investigating the genetic variations underlying diverse bacterial phenotypes at the population genome level. This review provides a comprehensive overview of the application of BGWAS in elucidating genetic determinants of bacterial drug resistance, pathogenicity, host specificity, biofilm formation, and probiotic fermentation characteristics. We systematically summarize the BGWAS workflow, including study design, data analysis pipelines, and the bioinformatics software employed at various stages. Furthermore, we highlight specialized tools tailored for BGWAS and discuss their unique features and applications. We also discuss confounding factors that can influence the accuracy and reliability of BGWAS results, including population structure, linkage disequilibrium, and multiple testing. By incorporating recent advancements, this review serves as a comprehensive reference for researchers utilizing BGWAS to uncover the genetic basis of bacterial phenotypes.
随着高通量基因组测序技术的不断进步以及创新生物信息学工具的发展，细菌全基因组关联研究（BGWAS）已成为一种变革性方法，用于在群体基因组水平上研究多种细菌表型背后的遗传变异。本综述全面概述了BGWAS在阐明细菌耐药性、致病性、宿主特异性、生物膜形成和益生菌发酵特性的遗传决定因素方面的应用。我们系统地总结了BGWAS工作流程，包括研究设计、数据分析管道以及在各个阶段使用的生物信息学软件。此外，我们重点介绍了为BGWAS量身定制的专门工具，并讨论了它们的独特特征和应用。我们还讨论了可能影响BGWAS结果准确性和可靠性的混杂因素，包括群体结构、连锁不平衡和多重检验。通过纳入最新进展，本综述为利用BGWAS揭示细菌表型遗传基础的研究人员提供了全面的参考。
