人工合成微生物组的构建与应用

徐昭勇; 胡海洋; 许平; 唐鸿志

doi:10.12211/2096-8280.2020-062

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人工合成微生物组的构建与应用

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- 人工合成微生物组的构建与应用
- Development and application of synthetic microbiome
- 合成生物学 2021年2卷第2期页码：181-193
- 作者机构：
  
  上海交通大学生命科学技术学院，微生物代谢国家重点实验室，上海 200240
- 作者简介：
  
  [ "徐昭勇(1996—)，男，博士研究生，主要研究方向为微生物降解多环芳烃、杂环污染物的分子机理研究。E-mail：xuzhaoyong@sjtu.edu.cn" ]
  [ "唐鸿志（1980—），男，教授，博士，主要研究方向为：微生物降解多环芳烃、杂环污染物的分子机理研究；环境微生物组学；合成生物学在环境修复中的应用。E-mail：tanghongzhi@sjtu.edu.cn" ]
- 基金信息：
  
  上海市2017年度“创新行动计划”基础研究重点项目(17JC1403300);上海市曙光计划(17SG09);上海市优秀学术带头人(20XD1421900);国家重点研发计划(2018YFA0901200)
- DOI：10.12211/2096-8280.2020-062
  中图分类号： Q932
- 收稿：2020-04-30，
  
  修回：2021-01-17，
  
  纸质出版：2021-04-30
- 稿件说明：
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徐昭勇, 胡海洋, 许平, 唐鸿志. 人工合成微生物组的构建与应用[J]. 合成生物学, 2021, 2(2): 181-193

XU Zhaoyong, HU Haiyang, XU Ping, TANG Hongzhi. Development and application of synthetic microbiome[J]. Synthetic Biology Journal, 2021, 2(2): 181-193
徐昭勇, 胡海洋, 许平, 唐鸿志. 人工合成微生物组的构建与应用[J]. 合成生物学, 2021, 2(2): 181-193 DOI： 10.12211/2096-8280.2020-062.

XU Zhaoyong, HU Haiyang, XU Ping, TANG Hongzhi. Development and application of synthetic microbiome[J]. Synthetic Biology Journal, 2021, 2(2): 181-193 DOI： 10.12211/2096-8280.2020-062.

摘要

近年来，随着微生物组学、计算生物学、合成生物学等研究的迅猛发展，人工构建高效稳定的人工菌群逐渐成为研究热点，从而衍生出新的研究领域，被称为合成微生物组。合成微生物组的研究，是通过对不同的微生物菌株进行整合，高效、稳定、安全地处理更复杂的任务，完成单一菌株无法完成的目标，从而满足更广泛的需要。本文简述了构建合成微生物组需要遵循的基本原则、四种策略，回答如何构建微生物组的问题，介绍了“自下而上”和“自上而下”两种构建合成微生物组的方法，回顾了合成微生物组在工业生产和环境修复领域的具体应用，例如生物能源、化工产品、生物医药的合成，以及石油、石油衍生物、农药等污染物的生物修复，为微生物技术的实际应用开拓了新的方向。最后，通过综合分析表明，挖掘代谢信息明确的合成微生物组底盘菌株并加以遗传改造，使其适应更复杂的环境，将是未来的研究重点。

Abstract

In recent years

the construction of artificial bacterial communities

usually referred to "synthetic” or “engineered” microbiomes

with better attributes and stability

has been a hot topic. The archetype synthetic community integrates different strains by balancing their nutrition

which occurs when strains produce and consume essential nutrients in a complementary fashion. Other key features of synthetic communities include: reciprocal interactions of metabolic pathways. On the one hand

complete metabolic pathways may develop only at the population level

and the metabolic burden on any single strain can reduce. On the other hand

growth inhibition can relief

since metabolites of one strain promote the growth of another

and reduction of the mutation rate guarantees a stable community. When combined

these features ensure intercellular interactions

spatiotemporal organization

community robustness

and biocontainment of synthetic communities. There are two general approaches for engineering microbiomes. One is "bottom-up"

through which genetic circuits involving different strains are designed artificially. This approach can be more controllable

but the precise knowledge of metabolic pathway details is needed. Another approach

known as "top-down"

involves the careful optimization of a core consortium from a group of natural microbiomes which can be easier to carry out

but is less designable. Synthetic microbiomes can be expected to handle complex tasks more efficiently

stably

and safely

which show a series of special characters compared with one single strain

such as apparent metabolic burden reduction and offering a platform with excellent compatibility for the expression of diverse genes. By now

the synthetic microbiome approach has already been applied to industrial production and environmental remediation

such as the biosynthesis of biofuels

chemical products

and biomedicines

and for the bioremediation of petroleum contamination and residues of petroleum derivatives and pesticides. Synthetic microbiomes open a new direction for applications of microbial technology with improved stability and compatibility. This approach could be used to enhance the roles of particularly valuable strains

helping to extend their applications to more complicated tasks in extreme environments.

关键词

Keywords

references

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