Research progress in construction of functional microbial communities

HUANG Jiacheng; ZHANG Aihui; FU Yousi; FANG Baishan

doi:10.12211/2096-8280.2021-074

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Research progress in construction of functional microbial communities

Invited Review | 更新时间：2025-03-20

- Research progress in construction of functional microbial communities
- Synthetic Biology Journal Vol. 3, Issue 1, Pages: 155-167(2022)
- 作者机构：
  
  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
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8280.2021-074
  CLC： Q 816
- Received：12 July 2021，
  
  Revised：2021-11-25，
  
  Published：28 February 2022
- 稿件说明：
移动端阅览
黄佳城，张瑷珲，付友思，方柏山. 功能性菌群构建的研究进展［J］. 合成生物学， 2022， 3（1）： 155-167

HUANG Jiacheng， ZHANG Aihui， FU Yousi， FANG Baishan. Research progress in construction of functional microbial communities［J］. Synthetic Biology Journal， 2022， 3（1）： 155-167
黄佳城，张瑷珲，付友思，方柏山. 功能性菌群构建的研究进展［J］. 合成生物学， 2022， 3（1）： 155-167 DOI： 10.12211/2096-8280.2021-074.

HUANG Jiacheng， ZHANG Aihui， FU Yousi， FANG Baishan. Research progress in construction of functional microbial communities［J］. Synthetic Biology Journal， 2022， 3（1）： 155-167 DOI： 10.12211/2096-8280.2021-074.

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。

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.

关键词

Keywords

references

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