Biofoundry and its industrial application

doi:10.12211/2096-8280.2023-024

Abstract

Abstract:

Traditional methods for strain isolation and improvement can be cumbersome, time-consuming, error-prone, and difficult to scale up, leading to inefficiencies in research and development workflows. With the integration of automation and robotics technology, biofoundry can achieve automated operations through guide rails and robotic arms, leading to improved stability and precision of experimental operations. Additionally, by utilizing smaller cultivation volumes, such as microplates or droplets, the cultivation and screening throughput can be increased, addressing the currently existing issues of traditional methods. This can greatly improve research and development efficiency, allowing for the testing and optimization of large numbers of microbial strains or genetic variants in a high-throughput manner. The biofoundry encompasses interdisciplinary fields such as mechanical engineering, automation, computer science, and life sciences. The collaboration among these fields is crucial for the development and advancement of laboratory automation. By leveraging automation and high-throughput technologies, the field of strain isolation and improvement can benefit from increased efficiency, improved reliability, and scalability. These advancements can accelerate the progress of microbial strain engineering for various applications in biotechnology, medicine, agriculture, and energy production. This paper briefly introduces the composition and classification of the biofoundry, the high-throughput detection method, and focuses on the high-throughput screening platform built by the research team from Nutrition & Health Research Institute, COFCO. In combination with the projects carried out, it introduces the application of the high-throughput screening platform in the fields of biofuel strain development, traditional brewing strain screening, feed substitute antimicrobial screening, directed evolution and screening of enzymes, etc.

Key words: biofoundry, automation, high-throughput screening, strain improvement, industrial microorganism

摘要：

传统菌株改造和筛选实验存在操作烦琐、耗时、易错、难以规模化等问题，生物设施平台将自动化、机器人技术、数据分析与生物研究相结合，通过导轨和机械手臂实现自动化操作，提高了实验操作的稳定性，通过缩小培养体积（微孔板或微液滴），提高了培养和筛选通量，解决了上述问题，大大提高了研发效率。本文简单介绍了自动化设施平台的发展和常见的高通量检测方法，重点介绍了中粮营养健康研究院的自动化设施平台，并结合开展的项目叙述了平台在生物燃料菌株开发、传统酿造菌株筛选、酶的定向进化和筛选等领域的应用，可以预见自动化和高通量化在菌株改造和筛选方向巨大的应用价值。实验室自动化是涉及机械工程、自动化、计算机和生命科学等学科的交叉领域，需要各方面共同努力，才能推动实验室向更高程度的自动化和智能化方向发展。

关键词: 生物设施平台, 自动化, 高通量筛选, 菌株改造, 工业微生物

CLC Number:

Q819

Guomiao ZHAO, Xin YANG, Yuan ZHANG, Jing WANG, Jian TAN, Chao WEI, Nana ZHOU, Fan LI, Xiaoyan WANG. Biofoundry and its industrial application[J]. Synthetic Biology Journal, 2023, 4(5): 892-903.

赵国淼, 杨鑫, 张媛, 王靖, 谭剑, 魏超, 周娜娜, 李凡, 王小艳. 生物设施平台及其工业应用[J]. 合成生物学, 2023, 4(5): 892-903.

Figures/Tables 7

Fig.1 Illinois Biological Foundry for Advanced Biomanufacturing (iBioFAB)

Fig. 2 Automated biofoundry at COFCO

Table 1 Comparison of three screening methods

筛选方法	检测信号	灵敏度	通量
MTP^[48]	吸光度和荧光强度	一般	10⁶个/天
FACS^[49]	荧光强度	高	10⁸个/时
DMF^[50]	荧光强度、拉曼光谱、吸光度、质谱	高	10⁸个/天

Fig.3 Improvement of Saccharomyces cerevisiae for multiple stress tolerance

Fig. 4 Application of high-throughput platform in traditional strain screening

Fig. 5 Application of the biofoundry in directed evolution and screening of EUGT11

Fig. 6 Application of biofoundry in directed evolution and screening of mycotoxins degrading enzymes

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