CRISPR-Cas基因编辑技术在微生物组工程中的应用

Applications of CRISPR-Cas Technologies in Microbiome Engineering

微生物组工程是对复杂微生物群落进行改造,在基因组、代谢组及群落生态结构等多个层次上实现微生物组的精准调控.成簇规律间隔短回文序列(CRISPR)及其相关蛋白(CRISPR-Cas)系统是近期发展迅速的高效基因编辑工具.本文回顾了微生物组工程领域CRISPR-Cas系统的重要研究工作,重点关注CRISPR-Cas系统在微生物组的基因编辑和生态调控方面的应用.针对CRISPR-Cas系统在微生物组工程领域的应用挑战,本文从外源DNA递送方式和基因表达调控元件两个方面总结了微生物组工程的关键辅助方法与发展趋势,展望了微生物组工程领域所面临的挑战与机遇.

Microbiome engineering aims to achieve targeted and precise manipulation of complex microbial communities.Clustered regularly interspaced short palindromic repeats(CRISPR)-CRISPR-associated protein(CRISPRCas)system is an emerging powerful tool for gene editing,which provides a probability to engineering microbiome from gene to ecosystem level.In this review,we summarize recent developments in the emerging area of microbiome engineering,focusing on the applications of CRISPR-Cas technologies in genetic manipulation of microbiome.To begin with,we introduce the concept of microbiome engineering.We propose to classify microbiome engineering by:(1)manipulation at the ecological level,i.e.,alterations in community composition;(2)manipulation at the genetic level,i.e.,editing of metagenomes.Furthermore,manipulation of mcirobiomes at the genetic level can be achieved via different approaches:(1)genome engineering of cultured microbial isolates;(2)metgenome engineering in situ.CRISPR-Cas tools have important applications in microbiome engineering,including strain-specific deletion,transcriptome regulation,site-specific insertion in complex communities,and dissecting the contribution of a single gene in microbiome-host interaction.The complexity of microbiomes requires the development of assistive technologies,such as highly efficient delivery methods,controllable genetic regulatory elements,etc.Finally,we discuss the challenges and opportunities in microbiome engineering,an emerging research area at the intersection of synthetic biology,chemical biology and microbiome.Breakthroughs in microbiome engineering will greatly advance our understanding of microbiome and transform many fields such as human health,agriculture,and environmental protection.