School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
Zhejiang Institute of Tianjin University, Shaoxing, 312300, China.
FEMS Microbiol Rev. 2024 Nov 23;48(6). doi: 10.1093/femsre/fuae026.
Microbes compete and cooperate with each other via a variety of chemicals and circuits. Recently, to decipher, simulate, or reconstruct microbial communities, many researches have been engaged in engineering microbiomes with bottom-up synthetic biology approaches for diverse applications. However, they have been separately focused on individual perspectives including genetic circuits, communications tools, microbiome engineering, or promising applications. The strategies for coordinating microbial ecosystems based on different regulation circuits have not been systematically summarized, which calls for a more comprehensive framework for the assembly of microbial communities. In this review, we summarize diverse cross-talk and orthogonal regulation modules for de novo bottom-up assembling functional microbial ecosystems, thus promoting further consortia-based applications. First, we review the cross-talk communication-based regulations among various microbial communities from intra-species and inter-species aspects. Then, orthogonal regulations are summarized at metabolites, transcription, translation, and post-translation levels, respectively. Furthermore, to give more details for better design and optimize various microbial ecosystems, we propose a more comprehensive design-build-test-learn procedure including function specification, chassis selection, interaction design, system build, performance test, modeling analysis, and global optimization. Finally, current challenges and opportunities are discussed for the further development and application of microbial ecosystems.
微生物通过各种化学物质和电路相互竞争和合作。最近，为了解码、模拟或重建微生物群落，许多研究人员采用自下而上的合成生物学方法来进行微生物组工程，以实现多样化的应用。然而，这些研究分别侧重于遗传电路、通信工具、微生物组工程或有前途的应用等个别方面。基于不同调控电路协调微生物生态系统的策略尚未得到系统总结，这需要一个更全面的微生物群落组装框架。在这篇综述中，我们总结了用于从头开始组装功能性微生物生态系统的各种交叉对话和正交调控模块，从而促进了基于群落的进一步应用。首先，我们从种内和种间两个方面回顾了各种微生物群落之间基于交叉对话的调控。然后，分别总结了代谢物、转录、翻译和翻译后水平的正交调控。此外，为了更详细地说明以便更好地设计和优化各种微生物生态系统，我们提出了一个更全面的设计-构建-测试-学习流程，包括功能规范、底盘选择、相互作用设计、系统构建、性能测试、建模分析和全局优化。最后，讨论了微生物生态系统进一步发展和应用的当前挑战和机遇。
