Assembly of functional microbial ecosystems: from molecular circuits to communities.

IF 10.1 2区 生物学 Q1 MICROBIOLOGY
Shengbo Wu, Yongsheng Zhou, Lei Dai, Aidong Yang, Jianjun Qiao
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引用次数: 0

Abstract

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.

功能微生物生态系统的组装:从分子电路到群落。
微生物通过各种化学物质和回路相互竞争与合作。最近,为了破译、模拟或重建微生物群落,许多研究人员都在利用自下而上的合成生物学方法进行微生物组工程研究,以实现各种应用。然而,这些研究分别侧重于不同的角度,包括遗传回路、通信工具、微生物组工程或有前景的应用。基于不同调控回路的微生物生态系统协调策略尚未得到系统总结,这就需要一个更全面的微生物群落组装框架。在这篇综述中,我们总结了用于自下而上重新组装功能微生物生态系统的各种交叉和正交调控模块,从而促进基于联合体的进一步应用。首先,我们从种内和种间两个方面综述了各种微生物群落之间基于串扰通讯的调控。然后,分别从代谢物、转录、翻译和翻译后水平总结了正交调控。此外,为了更详细地说明如何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(cDBTL)程序,包括功能说明、底盘选择、交互设计、系统构建、性能测试、建模分析和全局优化。最后,我们讨论了当前微生物生态系统进一步发展和应用所面临的挑战和机遇。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
FEMS microbiology reviews
FEMS microbiology reviews 生物-微生物学
CiteScore
17.50
自引率
0.90%
发文量
45
审稿时长
6-12 weeks
期刊介绍: Title: FEMS Microbiology Reviews Journal Focus: Publishes reviews covering all aspects of microbiology not recently surveyed Reviews topics of current interest Provides comprehensive, critical, and authoritative coverage Offers new perspectives and critical, detailed discussions of significant trends May contain speculative and selective elements Aimed at both specialists and general readers Reviews should be framed within the context of general microbiology and biology Submission Criteria: Manuscripts should not be unevaluated compilations of literature Lectures delivered at symposia must review the related field to be acceptable
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