高通量平行发酵技术的发展与应用

白仲虎; 任和; 聂简琪; 孙杨

doi:10.12211/2096-8280.2023-026

您当前的位置：

首页 >

文章列表页 >

高通量平行发酵技术的发展与应用

特约评述 | 更新时间：2025-03-20

- 高通量平行发酵技术的发展与应用
- The recent progresses and applications of in-parallel fermentation technology
- 合成生物学 2023年4卷第5期页码：904-915
- 作者机构：
  
  1.江南大学粮食发酵与食品生物制造国家工程研究中心，江苏无锡 214122
  2.河南大学生命科学学院，河南开封 475004
- 作者简介：
  
  [ "白仲虎（1965—），男，教授，博士生导师。研究方向为发酵工程、生物反应器、生物医药过程工程。E-mail：baizhonghu@jiangnan.edu.cn" ]
- 基金信息：
  
  国家高技术研究发展计划(2015A020802)
- DOI：10.12211/2096-8280.2023-026
  中图分类号： Q815
- 收稿：2023-03-30，
  
  修回：2023-06-25，
  
  纸质出版：2023-10-31
- 稿件说明：
移动端阅览
白仲虎，任和，聂简琪，孙杨. 高通量平行发酵技术的发展与应用［J］. 合成生物学， 2023， 4（5）： 904-915

BAI Zhonghu， REN He， NIE Jianqi， SUN Yang. The recent progresses and applications of in-parallel fermentation technology［J］. Synthetic Biology Journal， 2023， 4（5）： 904-915
白仲虎，任和，聂简琪，孙杨. 高通量平行发酵技术的发展与应用［J］. 合成生物学， 2023， 4（5）： 904-915 DOI： 10.12211/2096-8280.2023-026.

BAI Zhonghu， REN He， NIE Jianqi， SUN Yang. The recent progresses and applications of in-parallel fermentation technology［J］. Synthetic Biology Journal， 2023， 4（5）： 904-915 DOI： 10.12211/2096-8280.2023-026.

摘要

21世纪初，为解决生物医药过程工程研究所面临的微生物和哺乳动物细胞培养的实验通量、研发效率与成本方面的问题，更重要的是质量源于设计（QbD）导向的生物过程工程实验设计（DoE）的迫切需要，基于微、小型生物反应器的平行发酵（细胞培养）技术与产品得到了广泛应用。近年来微生物代谢工程与合成生物学的飞速发展，对高性能菌种库的高通量筛选与菌种表型过程表现的早期评价提出了更高实验通量的需求，这进一步拓展了不同培养体积的平行发酵培养装置在工业生物技术领域的应用。时至今日，可模拟工业培养条件并实施过程参数准确控制的微小型反应器的多联罐平行发酵装置、系统操作软件和数据处理的集成系统已成为生物过程工程研发的强大工具，它在生物医药创新、代谢工程和合成生物学等基础研究成果向工业化技术转化中起到重要的支撑作用。特别是在合成生物学领域中，基于“工业相似性“原则的平行发酵技术，可以解决培养板或摇瓶高通量菌种筛选无法表征克隆表型、在规模化培养中的表现受培养过程参数显著影响的痛点问题，实现过程工程导向的高通量、高效率的菌种筛选与评价。本文对高通量平行发酵与细胞培养技术的发展近况与其在合成生物学研究中的应用场景做了介绍，其中主要总结了平行发酵培养技术在高通量菌种筛选评价“三段论”中的价值、平行发酵培养如何支持菌种筛选的工业相似性原则的实施、平行发酵培养结合DoE实验策略实施高效的生物过程工程开发、使用平行发酵培养建立过程多变元批次模型的方法，以及平行发酵培养与建立生物培养过程缩小模型的关系等。

Abstract

At the beginning of this century

high-throughput in-parallel fermentation (cell culture) technology and its related apparatus based on microbioreactor and miniature bioreactor were developed and widely applied. This was to solve the challenges encountered by biopharmaceutical process researches in terms of cultivation throughput

R&D efficiency

and the continuous rising on the cost for microbial fermentation and mammalian cell cultures of multiple clones

and more importantly

the urgent needs for conducting design of experiment (DoE) driven by the principle of quality by design (QbD). In the recent years

the rapid advance of microbial metabolic engineering and synthetic biology has put forward a rather strong demands for the high-throughput screening on high-performance strain libraries and the early evaluation of strain phenotypic potential performance under industrial cultivation conditions. This has further expanded the application range of in-parallel fermentation technology with various culture volumes in the field of modern industrial biotechnology. Up to now

integrated systems containing in-parallel fermentation setups with multiple microbioreactors

online probes

operating software

and data processing units

which can simulate industrial cultivation conditions and implement accurate control of process parameters

have become a powerful tool for accelerating bioprocesses engineering R&D. They play a central role in transforming basic research achievements

such as drug discovery

metabolic engineering

and synthetic biology

into industrial technologies. Especially in the field of synthetic biology

based on the principle of "industrial similarity"

in-parallel fermentation technology addresses key limitations of the conventional microplate and shake flask based high throughput screening

which cannot characterize the significant impact of culture conditions on the phenotypic performance of the selected clones at a large scale. This enables a process-oriented

high throughput

and efficient screening and evaluation if microbial strain libraries. This review provides an overview on the recent development in high throughput in-parallel fermentation & cell culture technology and its application scenarios of synthetic biology researches. In particular

it emphasizes the value of in-parallel fermentation technology in high-throughput strain screening complying with the three-stage strategy

and how in-parallel fermentation technology makes the implementation of the industrial similarity principle of strain screening possible

and how the technology combines DoE experimental tactic to significantly improve the efficiency of bioprocess development. It is also discussed the general procedure to build up a multivariate batch model of bioprocess based on in-parallel fermentation technology. In the end the approach of using in-parallel culture to establish a process scale down model is also explored.

关键词

Keywords

references

RIENZO M , JACKSON S J , CHAO L K , et al . High-throughput screening for high-efficiency small-molecule biosynthesis [J ] . Metabolic Engineering , 2021 , 63 : 102 - 125 .

AKKERMANS S , NIMMEGEERS P , VAN IMPE J F . Comparing design of experiments and optimal experimental design techniques for modelling the microbial growth rate under static environmental conditions [J ] . Food Microbiology , 2018 , 76 : 504 - 512 .

WALSH I , MYINT M , NGUYEN-KHUONG T , et al . Harnessing the potential of machine learning for advancing "Quality by Design" in biomanufacturing [J ] . mAbs , 2022 , 14 ( 1 ): 2013593 .

ICH Q 8( R 2). Pharmaceutical Development [EB/OL ] . 2009[ 2023-03-01 ] . https://max.book118.com/html/2019/0805/5044012342002112.shtm https://max.book118.com/html/2019/0805/5044012342002112.shtm .

LIAO X P , MA H W , TANG Y J . Artificial intelligence: a solution to involution of design-build-test-learn cycle [J ] . Current Opinion in Biotechnology , 2022 , 75 : 102712 .

ORSI E , BEEKWILDER J , EGGINK G , et al . The transition of Rhodobacter sphaeroides into a microbial cell factory [J ] . Biotechnology and Bioengineering , 2021 , 118 ( 2 ): 531 - 541 .

FLETCHER E , CHEN Y , CASPETA L , et al . Editorial: genomic strategies for efficient microbial cell factories [J ] . Frontiers in Bioengineering and Biotechnology , 2022 , 10 : 962828 .

GURDO N , VOLKE D C , MCCLOSKEY D , et al . Automating the design-build-test-learn cycle towards next-generation bacterial cell factories [J ] . New Biotechnology , 2023 , 74 : 1 - 15 .

NAKAZAWA S , IMAICHI O , KOGURE T , et al . History-driven genetic modification design technique using a domain-specific lexical model for the acceleration of DBTL cycles for microbial cell factories [J ] . ACS Synthetic Biology , 2021 , 10 ( 9 ): 2308 - 2317 .

ISETT K , GEORGE H , HERBER W , et al . Twenty-four-well plate miniature bioreactor high-throughput system: assessment for microbial cultivations [J ] . Biotechnology and Bioengineering , 2007 , 98 ( 5 ): 1017 - 1028 .

MÜHLMANN M , KUNZE M , RIBEIRO J , et al . Cellulolytic RoboLector-towards an automated high-throughput screening platform for recombinant cellulase expression [J ] . Journal of Biological Engineering , 2017 , 11 ( 1 ): 1 .

VELEZ-SUBERBIE M L , BETTS J P J , WALKER K L , et al . High throughput automated microbial bioreactor system used for clone selection and rapid scale-down process optimization [J ] . Biotechnology Progress , 2018 , 34 ( 1 ): 58 - 68 .

HEMMERICH J , NOACK S , WIECHERT W , et al . Microbioreactor systems for accelerated bioprocess development [J ] . Biotechnology Journal , 2018 , 13 ( 4 ): 1700141 .

ABATE A R , HUNG T , MARY P , et al . High-throughput injection with microfluidics using picoinjectors [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2010 , 107 ( 45 ): 19163 - 19166 .

BROMIG L , VON DEN EICHEN N , WEUSTER-BOTZ D . Control of parallelized bioreactorsⅠ: dynamic scheduling software for efficient bioprocess management in high-throughput systems [J ] . Bioprocess and Biosystems Engineering , 2022 , 45 ( 12 ): 1927 - 1937 .

LONG Q , LIU X X , YANG Y K , et al . The development and application of high throughput cultivation technology in bioprocess development [J ] . Journal of Biotechnology , 2014 , 192 Pt B: 323- 338 .

SANDNER V , PYBUS L P , MCCREATH G , et al . Scale-down model development in ambr systems: an industrial perspective [J ] . Biotechnology Journal , 2019 , 14 ( 4 ): 1700766 .

CRUZ BOURNAZOU M N , BARZ T , NICKEL D B , et al . Online optimal experimental re-design in robotic parallel fed-batch cultivation facilities [J ] . Biotechnology and Bioengineering , 2017 , 114 ( 3 ): 610 - 619 .

JANSEN R , TENHAEF N , MOCH M , et al . FeedER: a feedback-regulated enzyme-based slow-release system for fed-batch cultivation in microtiter plates [J ] . Bioprocess and Biosystems Engineering , 2019 , 42 ( 11 ): 1843 - 1852 .

HEMMERICH J , WIECHERT W , OLDIGES M . Automated growth rate determination in high-throughput microbioreactor systems [J ] . BMC Research Notes , 2017 , 10 ( 1 ): 617 .

MORSCHETT H , JANSEN R , NEUENDORF C , et al . Parallelized microscale fed-batch cultivation in online-monitored microtiter plates: implications of media composition and feed strategies for process design and performance [J ] . Journal of Industrial Microbiology & Biotechnology , 2020 , 47 ( 1 ): 35 - 47 .

HEMMERICH J , TENHAEF N , STEFFENS C , et al . Less sacrifice, more insight: repeated low-volume sampling of microbioreactor cultivations enables accelerated deep phenotyping of microbial strain libraries [J ] . Biotechnology Journal , 2019 , 14 ( 9 ): 1800428 .

UNTHAN S , RADEK A , WIECHERT W , et al . Bioprocess automation on a Mini Pilot Plant enables fast quantitative microbial phenotyping [J ] . Microbial Cell Factories , 2015 , 14 : 32 .

LAWSON C E , HARCOMBE W R , HATZENPICHLER R , et al . Common principles and best practices for engineering microbiomes [J ] . Nature Reviews Microbiology , 2019 , 17 ( 12 ): 725 - 741 .

ZHU X F , DU C C , MOHSIN A , et al . An efficient high-throughput screening of high gentamicin-producing mutants based on titer determination using an integrated computer-aided vision technology and machine learning [J ] . Analytical Chemistry , 2022 , 94 ( 33 ): 11659 - 11669 .

KAMMINGA T , SLAGMAN S J , MARTINS DOS SANTOS V A P , et al . Risk-based bioengineering strategies for reliable bacterial vaccine production [J ] . Trends in Biotechnology , 2019 , 37 ( 8 ): 805 - 816 .

LIU Y , NIELSEN J . Recent trends in metabolic engineering of microbial chemical factories [J ] . Current Opinion in Biotechnology , 2019 , 60 : 188 - 197 .

SARNAIK A , LIU A , NIELSEN D , et al . High-throughput screening for efficient microbial biotechnology [J ] . Current Opinion in Biotechnology , 2020 , 64 : 141 - 150 .

ZENG W Z , GUO L K , XU S , et al . High-throughput screening technology in industrial biotechnology [J ] . Trends in Biotechnology , 2020 , 38 ( 8 ): 888 - 906 .

RAJ K , VENAYAK N , DIEP P , et al . Automation assisted anaerobic phenotyping for metabolic engineering [J ] . Microbial Cell Factories , 2021 , 20 ( 1 ): 184 .

RIENZO M , LIN K C , MOBILIA K C , et al . High-throughput optofluidic screening for improved microbial cell factories via real-time micron-scale productivity monitoring [J ] . Lab on a Chip , 2021 , 21 ( 15 ): 2901 - 2912 .

POLITIS S N , COLOMBO P , COLOMBO G , et al . Design of experiments (DoE) in pharmaceutical development [J ] . Drug Development and Industrial Pharmacy , 2017 , 43 ( 6 ): 889 - 901 .

SWAIN S , PARHI R , JENA B R , et al . Quality by design: concept to applications [J ] . Current Drug Discovery Technologies , 2019 , 16 ( 3 ): 240 - 250 .

NOLD V , JUNGHANS L , BISGEN L , et al . Applying intensified design of experiments to mammalian cell culture processes [J ] . Engineering in Life Sciences , 2022 , 22 ( 12 ): 784 - 795 .

TAI M , LY A , LEUNG I , et al . Efficient high-throughput biological process characterization: definitive screening design with the ambr250 bioreactor system [J ] . Biotechnology Progress , 2015 , 31 ( 5 ): 1388 - 1395 .

PEREIRA R F S , DE CARVALHO C C C R . Optimization of multiparameters for increased yields of cytochrome B5 in bioreactors [J ] . Molecules , 2021 , 26 ( 14 ): 4148 .

MERCIER S M , DIEPENBROEK B , DALM M C F , et al . Multivariate data analysis as a PAT tool for early bioprocess development data [J ] . Journal of Biotechnology , 2013 , 167 ( 3 ): 262 - 270 .

MERCIER S M , DIEPENBROEK B , WIJFFELS R H , et al . Multivariate PAT solutions for biopharmaceutical cultivation: current progress and limitations [J ] . Trends in Biotechnology , 2014 , 32 ( 6 ): 329 - 336 .

RATHORE A S , MITTAL S , PATHAK M , et al . Guidance for performing multivariate data analysis of bioprocessing data: pitfalls and recommendations [J ] . Biotechnology Progress , 2014 , 30 ( 4 ): 967 - 973 .

XU P , CLARK C , RYDER T , et al . Characterization of TAP Ambr 250 disposable bioreactors, as a reliable scale-down model for biologics process development [J ] . Biotechnology Progress , 2017 , 33 ( 2 ): 478 - 489 .

NIKITA S , MISHRA S , GUPTA K , et al . Advances in bioreactor control for production of biotherapeutic products [J ] . Biotechnology and Bioengineering , 2023 , 120 ( 5 ): 1189 - 1214 .

SÃO PEDRO M N , SILVA T C , PATIL R , et al . White paper on high-throughput process development for integrated continuous biomanufacturing [J ] . Biotechnology and Bioengineering , 2021 , 118 ( 9 ): 3275 - 3286 .

KHANAL O , LENHOFF A M . Developments and opportunities in continuous biopharmaceutical manufacturing [J ] . mAbs , 2021 , 13 ( 1 ): 1903664 .

ANANE E , GARCÍA Á C , HABY B , et al . A model-based framework for parallel scale-down fed-batch cultivations in mini-bioreactors for accelerated phenotyping [J ] . Biotechnology and Bioengineering , 2019 , 116 ( 11 ): 2906 - 2918 .

TAPIA F , VÁZQUEZ-RAMÍREZ D , GENZEL Y , et al . Bioreactors for high cell density and continuous multi-stage cultivations: options for process intensification in cell culture-based viral vaccine production [J ] . Applied Microbiology and Biotechnology , 2016 , 100 ( 5 ): 2121 - 2132 .

JANOSCHEK S , SCHULZE M , ZIJLSTRA G , et al . A protocol to transfer a fed-batch platform process into semi-perfusion mode: the benefit of automated small-scale bioreactors compared to shake flasks as scale-down model [J ] . Biotechnology Progress , 2019 , 35 ( 2 ): e2757 .

LIN H , LEIGHTY R W , GODFREY S , et al . Principles and approach to developing mammalian cell culture media for high cell density perfusion process leveraging established fed-batch media [J ] . Biotechnology Progress , 2017 , 33 ( 4 ): 891 - 901 .

XU J L , OU J F , MCHUGH K P , et al . Upstream cell culture process characterization and in-process control strategy development at pandemic speed [J ] . mAbs , 2022 , 14 ( 1 ): 2060724 .

WOLF M K F , LORENZ V , KARST D J , et al . Development of a shake tube-based scale-down model for perfusion cultures [J ] . Biotechnology and Bioengineering , 2018 , 115 ( 11 ): 2703 - 2713 .

MACDONALD M A , NÖBEL M , ROCHE RECINOS D , et al . Perfusion culture of Chinese Hamster Ovary cells for bioprocessing applications [J ] . Critical Reviews in Biotechnology , 2022 , 42 ( 7 ): 1099 - 1115 .

KUIPER M , SPENCER C , FÄLDT E , et al . Repurposing fed-batch media and feeds for highly productive CHO perfusion processes [J ] . Biotechnology Progress , 2019 , 35 ( 4 ): e2821 .

JANAKIRAMAN V , KWIATKOWSKI C , KSHIRSAGAR R , et al . Application of high-throughput mini-bioreactor system for systematic scale-down modeling, process characterization, and control strategy development [J ] . Biotechnology Progress , 2015 , 31 ( 6 ): 1623 - 1632 .

浏览量

下载量

CSCD

文章被引用时，请邮件提醒。

提交

工具集

关联资源

功能肽合成和挖掘策略研究进展

超声移液及微量移液技术进展和展望

细胞培养肉用生物材料的设计