Common principles and best practices for engineering microbiomes.,Nature Reviews Microbiology

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Common principles and best practices for engineering microbiomes.
Nature Reviews Microbiology ( IF 69.2 ) Pub Date : 2019-09-23 , DOI: 10.1038/s41579-019-0255-9
Christopher E Lawson ₁ , William R Harcombe ₂ , Roland Hatzenpichler _{3,

4,

5} , Stephen R Lindemann ₆ , Frank E Löffler _{7,

8} , Michelle A O'Malley _{9,

10} , Héctor García Martín _{10,

11,

12,

13} , Brian F Pfleger ₁₄ , Lutgarde Raskin ₁₅ , Ophelia S Venturelli _{14,

16,

17} , David G Weissbrodt ₁₈ , Daniel R Noguera _{1,

19} , Katherine D McMahon _{1,

17}

Affiliation

Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA.
Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, USA.
Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA.
Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
Department of Food Sciences, Purdue University, West Lafayette, IN, USA.
Center for Environmental Biotechnology, University of Tennessee-Knoxville, Knoxville, TN, USA.
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbra, CA, USA.
DOE Joint Bioenergy Institute, Emeryville, CA, USA.
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
DOE Agile BioFoundry, Emeryville, CA, USA.
Basque Center for Applied Mathematics, Bilbao, Spain.
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, USA.
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
Department of Biotechnology, Delft University of Technology, Delft, Netherlands.
DOE Great Lakes Bioenergy Research Center, Madison, WI, USA.

Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges. We argue that structuring research and technology developments around a design-build-test-learn (DBTL) cycle will advance microbiome engineering and spur new discoveries of the basic scientific principles governing microbiome function. In this Review, we present key elements of an iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches, including top-down and bottom-up design processes, synthetic and self-assembled construction methods, and emerging tools to analyse microbiome function. These approaches can be used to harness microbiomes for broad applications related to medicine, agriculture, energy and the environment. We also discuss key challenges and opportunities of each approach and synthesize them into best practice guidelines for engineering microbiomes. We anticipate that adoption of a DBTL framework will rapidly advance microbiome-based biotechnologies aimed at improving human and animal health, agriculture and enabling the bioeconomy.

中文翻译：

微生物组工程的共同原则和最佳实践。

尽管科学界对利用地球微生物群的力量产生了广泛的兴趣，但知识差距阻碍了其有效利用来解决紧迫的社会和环境挑战。我们认为，围绕设计-构建-测试-学习 (DBTL) 循环构建研究和技术开发将推进微生物组工程，并刺激控制微生物组功能的基本科学原理的新发现。在这篇综述中，我们介绍了微生物组工程迭代 DBTL 循环的关键要素，重点关注可推广的方法，包括自上而下和自下而上的设计过程、合成和自组装的构建方法以及分析微生物组功能的新兴工具。这些方法可用于利用微生物组进行与医学、农业、能源和环境相关的广泛应用。我们还讨论了每种方法的主要挑战和机遇，并将它们综合成工程微生物组的最佳实践指南。我们预计，采用 DBTL 框架将迅速推进基于微生物组的生物技术，旨在改善人类和动物健康、农业和促进生物经济。

更新日期：2019-09-23

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