合成微生物群落的构建与应用

Design and application of synthetic microbial communities

自然界中微生物群落的生态网络结构非常复杂,并且难以进行可重复、可控的扰动实验.在实验室里通过“自下而上”的方式构建起来的合成群落具有适中的复杂度和较高的可控性,可以作为数学模型和复杂生态系统研究之间的桥梁.合成微生物群落的研究方法遵循“设计-构建-测试-学习”为核心的合成生物学理念,以人工设计和构建的群落为实验对象,结合定量模型和基因组测序等组学技术,探索微生物生态学的基本规律.在应用方面,基于合成群落的研究对于如何控制和改造复杂的微生物生态系统具有重要的指导意义,目标是通过构建具有可控功能和稳定性的微生物群落来解决人体健康、农业和工业生产、环境治理等重要问题.

Microorganisms are ubiquitous in our world,and they form different communities between organisms and the surrounding environment.It is estimated that there are more than 108 bacteria in a small gram of soil,and there are more than 1013 bacteria in the human intestine.It is a complex ecosystem formed under the interaction mechanisms of resource competition,nutrient symbiosis,quorum sensing,and horizontal gene transfer.Among them,the microbial communities in the soil and hydrosphere environment play a key driving role in the global chemical cycle of carbon,nitrogen and other elements.In industrial production,the microbial communities can treat our waste and purify the environment.In the field of human diseases,the microbial community in the human intestine is closely related to the development,metabolism and immunity of the host.Therefore,studying the stability of the composition of the microbial community is of great significance for solving the problems of ecological environment,agricultural production,and human health.With the development of high-throughput sequencing technology,the diversity and stability of microbial communities in different environments have been deeply studied.Although the scientific community has paid more attention to microbial communities in recent years,there are still many difficulties before us effectively use these communities to meet social requirements and environmental challenges.Therefore,it is critical to use new scientific concepts such as synthetic biology to interpret existing scientific problems.Among them,the core cycle of synthetic biology,Design-Build-Test-Learn is expected to promote the perfection and discovery of the basic theory of microbial ecological communities,and promote the research and development of biotechnology lays a theoretical foundation for improving the application of human health,agricultural production and environmental pollution.The ecology of microbial communities in nature is highly complex,making it challenging to carry out reproducible,controllable perturbation experiments in natural ecosystems.In contrast,synthetic communities constructed in the laboratory using a“bottom-up”approach offer moderate complexity and high controllability,and can serve as a bridge between complex ecosystems and mathematical modeling.By combining synthetic microbial communities,quantitative models and sequencing techniques,we can systematically study interactions between microbial populations and predict the dynamics of microbial communities.In terms of application,research on synthetic microbial communities will provide critical insights for how to control and engineer complex microbial ecosystems,and help solve important problems in human health and agricultural production via the design of stable microbial communities with controllable functions.In this review article,we mainly focus on the construction methods and theoretical foundations of existing synthetic microbial communities and the potential applications of these communities from two aspects,namely the knowledge of creation and the application of creation.And we also discuss the potential application of synthetic biology methods in this field.