基于宏基因组测序的细菌株水平研究进展

Strain-level bacterial analysis from shotgun metagenomics:a review

宏基因组指样本中全部生物遗传物质的集合。目前,细菌的宏基因组学研究主要包含群落组成结构、遗传多样性以及重要功能基因谱等内容,相关分析通常基于细菌的属或种水平开展。随着高通量测序技术和生物信息学分析技术的发展,宏基因组研究已初步达到细菌株水平解析度,为推断细菌生态和进化规律等提供了新的工具和科学认识。本研究从遗传多样性、疫情暴发溯源研究以及重要功能基因谱3个方面,对基于宏基因组测序的细菌株水平研究进展进行了总结,以期为该技术的发展应用提供参考。

Identifying bacterial strains and characterizing their population,genetic variety and functional gene sets is essential for bacterial pathogen discovery,epidemiology,and infection control.With the development of high throughput sequencing and bioinformatics tools,we can characterize the individual bacterial strains in the context of complex community.In this review,we present the current works of strain-level bacterial analysis from metagenomics in three aspects:genetic diversity,outbreak tracing and functional gene profile.The work provides related references for the applications of bacterial analysis from metagenomics in clinical and environmental microbiology,and public health.