合成生物学 ›› 2022, Vol. 3 ›› Issue (1): 155-167.DOI: 10.12211/2096-8280.2021-074

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功能性菌群构建的研究进展

黄佳城1,2, 张瑷珲1,2, 付友思1,2, 方柏山1,2   

  1. 1.厦门大学化学化工学院,福建 厦门 361005
    2.厦门市合成生物技术重点实验室,福建 厦门 361005
  • 收稿日期:2021-07-12 修回日期:2021-11-25 出版日期:2022-02-28 发布日期:2022-03-14
  • 通讯作者: 方柏山
  • 作者简介:黄佳城(1997—),男,硕士研究生。研究方向为人工智能在合成生物学与宏基因组上的应用等。E-mail:chonpcaacpnohc@gmail.com
    方柏山(1957—),男,教授。研究方向为合成生物学与生物分子机器;定向进化与生物催化;生物技术过程开发与优化等。E-mail:fbs@xmu.edu.cn
  • 基金资助:
    国家自然科学基金(21978245);博士后创新人才支持计划(BX20200197)

Research progress in construction of functional microbial communities

Jiacheng HUANG1,2, Aihui ZHANG1,2, Yousi FU1,2, Baishan FANG1,2   

  1. 1.College of Chemistry and Chemical Engineering,Xiamen University,Xiamen 361005,Fujian,China
    2.The Key Laboratory for Synthetic Biotechnology of Xiamen City,Xiamen 361005,Fujian,China
  • Received:2021-07-12 Revised:2021-11-25 Online:2022-02-28 Published:2022-03-14
  • Contact: Baishan FANG

摘要:

功能性菌群构建作为一个新兴的研究方向,随着合成生物学、微生物组学技术的发展,逐渐成为研究热点。本文将从以下4个方面介绍功能性菌群的研究进展。第一,功能性菌群研究的初衷及其相对于单一生物体工程的优势和设计难点;第二,功能性菌群研究中自下而上(bottom-up)和自上而下(top-down)的设计策略;第三,功能性菌群的分析工具,包括“宏组学”和“多组学联用”手段以及相关的数据处理流程和软件。第四,分别从设计策略和分析工具方面出发,总结了功能性菌群构建过程中的主要挑战,并展望了未来以“智能设计”为核心的发展方向:①利用可解释的时空数据模型解析区域范围内功能性菌群的时空变化关系;②结合图神经网络与多模态学习方法建立多组学群落分析流程;③通过强化学习设计功能性菌群内分布式代谢回路。

关键词: 功能性菌群, 自下而上, 自上而下, 宏组学, 多组学, 智能设计

Abstract:

Study on functional microbial communities has become a hotspot with development of synthetic biology and microbiome. Comparing to single organism, functional microbial communities have several advantages in their robustness when facing environmental interference and for higher yields when producing complex products. This article introduces the research progress in studies on functional microbial communities from aspects: 1) the original motivation of functional microbial community research and the advantages and difficulties in design compared with single organism engineering, 2) the "bottom-up" and "top-down" strategies in the functional microbial community design process, and 3) analysis tools for functional microbial communities, such as "metagenomics", "multi-omics" and related data processing procedures and software. The main history of environmental microbial analysis is reviewed, and the main concepts of meta-omics is introduced. The major software which is used to process meta-omics data is also commented. In addition, challenges for the functional microbial community construction are highlighted based on the design strategy and analysis tools. The "bottom-up" strategy is not suitable for constructing a complicated microbial community, while the biosafety needs to be considered for developing the "top-down" strategy. Finally, the development of microbial communities with "intelligent design" as the core is prospected: first, using an interpretable spatiotemporal data model for temporal-spatial relationship mining of functional microbial communities; second, combining neural network and multi-modal learning methods to establish a multi-omics community analysis process; third, computational design of distributed metabolic circuits in the functional microbial community through reinforcement learning.

Key words: functional microbial community, bottom-up, top-down, meta-omics, multi-omics, intelligent design

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