1
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Fang S, Sinanan DJ, Perez MH, Cruz-Quintero RG, Jadhav SR. Development of a high-throughput scale-down model in Ambr® 250 HT for plasmid DNA fermentation processes. Biotechnol Prog 2024:e3458. [PMID: 38494959 DOI: 10.1002/btpr.3458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/28/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024]
Abstract
Recent advances in messenger ribonucleic acid (mRNA) vaccines and gene therapy vectors have increased the need for rapid plasmid DNA (pDNA) screening and production within the biopharmaceutical industry. High-throughput (HT) fermentor systems, such as the Ambr® 250 HT, can significantly accelerate process development timelines of pDNA upstream processes compared to traditional bench-scale glass fermentors or small-scale steam-in-place (SIP) fermentors. However, such scale-down models must be qualified to ensure that they are representative of the larger scale process similar to traditional small-scale models. In the current study, we developed a representative scale-down model of a Biostat® D-DCU 30 L pDNA fermentation process in Ambr® 250 HT fermentors using three cell lines producing three different constructs. The Ambr scale-down model provided comparable process performance and pDNA quality as the 30 L SIP fermentation process. In addition, we demonstrated the predictive value of the Ambr model by two-way qualification, first by accurately reproducing the prior trends observed in a 30 L process, followed by predicting new process trends that were then successfully reproduced in the 30 L process. The representative and predictive scale-down Ambr model developed in this study would enable a faster and more efficient approach to strain/clone/host-cell screening, pDNA process development and characterization studies, process scale-up studies, and manufacturing support.
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Affiliation(s)
- Shu Fang
- BioProcess Research & Development, Pfizer Inc., Chesterfield, Missouri, USA
| | - Dillon J Sinanan
- BioProcess Research & Development, Pfizer Inc., Chesterfield, Missouri, USA
| | - Marc H Perez
- BioProcess Research & Development, Pfizer Inc., Chesterfield, Missouri, USA
| | | | - Sachin R Jadhav
- BioProcess Research & Development, Pfizer Inc., Chesterfield, Missouri, USA
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2
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Moreno-Paz S, van der Hoek R, Eliana E, Martins Dos Santos VAP, Schmitz J, Suarez-Diez M. Combinatorial optimization of pathway, process and media for the production of p-coumaric acid by Saccharomyces cerevisiae. Microb Biotechnol 2024; 17:e14424. [PMID: 38528768 DOI: 10.1111/1751-7915.14424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 03/27/2024] Open
Abstract
Microbial cell factories are instrumental in transitioning towards a sustainable bio-based economy, offering alternatives to conventional chemical processes. However, fulfilling their potential requires simultaneous screening for optimal media composition, process and genetic factors, acknowledging the complex interplay between the organism's genotype and its environment. This study employs statistical design of experiments to systematically explore these relationships and optimize the production of p-coumaric acid (pCA) in Saccharomyces cerevisiae. Two rounds of fractional factorial designs were used to identify factors with a significant effect on pCA production, which resulted in a 168-fold variation in pCA titre. Moreover, a significant interaction between the culture temperature and expression of ARO4 highlighted the importance of simultaneous process and strain optimization. The presented approach leverages the strengths of experimental design and statistical analysis and could be systematically applied during strain and bioprocess design efforts to unlock the full potential of microbial cell factories.
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Affiliation(s)
- Sara Moreno-Paz
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Rianne van der Hoek
- Department of Science and Research-dsm-firmenich, Science & Research, Delft, The Netherlands
| | - Elif Eliana
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Joep Schmitz
- Department of Science and Research-dsm-firmenich, Science & Research, Delft, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
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3
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Iurashev D, Jones PA, Andreev N, Wang Y, Iwata-Kajihara T, Kraus B, Hernandez Bort JA. Scaling strategy for cell and gene therapy bioreactors based on turbulent parameters. Biotechnol J 2024; 19:e2300235. [PMID: 37906704 DOI: 10.1002/biot.202300235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/10/2023] [Accepted: 10/23/2023] [Indexed: 11/02/2023]
Abstract
So far, power input has been used as the main parameter for bioreactor scale-up/-down in upstream process development and manufacturing. The rationale is that maintaining a consistent power input per unit volume should result in comparable mixing times at different scales. However, shear generated from turbulent flow may compromise the integrity of non-robust cells such as those used during the production of cell and gene therapies, which may lead to low product quality and yield. Of particular interest is the Kolmogorov length parameter that characterizes the smallest turbulent eddies in a mixture. To understand its impact on scale-up/-down decisions, the distribution of Kolmogorov length along the trajectory flow of individual particles in bioreactors was estimated in silico with the help of computational fluid dynamics simulations. Specifically, in this study the scalability of iPSC-derived lymphocyte production and the impact of shear stress across various differentiation stages were investigated. The study used bioreactors of volumes from 0.1 to 10 L, which correspond to the scales most used for parameter optimization. Our findings, which align with in vitro runs, help determine optimal agitation speed and shear stress adjustments for process transfer between scales and bioreactor types, using vertically-oriented wheel and pitched-blade impellers. In addition, empirical models specific to the bioreactors used in this study were developed. The provided computational analysis in combination with experimental data supports selection of appropriate bioreactors and operating conditions for various cell and gene therapy process steps.
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Affiliation(s)
- Dmytro Iurashev
- Gene Therapy Process Development, Baxalta Innovations GmbH, a part of Takeda companies, Orth an der Donau, Austria
| | | | - Nadejda Andreev
- Cell Therapy, Takeda Pharmaceuticals USA, Cambridge, Massachusetts, USA
| | - Yana Wang
- Cell Therapy, Takeda Pharmaceuticals USA, Cambridge, Massachusetts, USA
| | - Tomoko Iwata-Kajihara
- Cell Therapy Process Development and Manufacturing, Takeda Pharmaceuticals Japan, Muraoka-Higashi, Fujisawa-shi, Kanagawa, Japan
| | - Barbara Kraus
- Gene Therapy Process Development, Baxalta Innovations GmbH, a part of Takeda companies, Orth an der Donau, Austria
| | - Juan A Hernandez Bort
- Gene Therapy Process Development, Baxalta Innovations GmbH, a part of Takeda companies, Orth an der Donau, Austria
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4
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Hoang MD, Polte I, Frantzmann L, von den Eichen N, Heins AL, Weuster-Botz D. Impact of mixing insufficiencies on L-phenylalanine production with an Escherichia coli reporter strain in a novel two-compartment bioreactor. Microb Cell Fact 2023; 22:153. [PMID: 37574555 PMCID: PMC10424407 DOI: 10.1186/s12934-023-02165-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 08/01/2023] [Indexed: 08/15/2023] Open
Abstract
BACKGROUND The omnipresence of population heterogeneity in industrial bioprocesses originates from prevailing dynamic bioprocess conditions, which promote differences in the expression of cellular characteristics. Despite the awareness, the concrete consequences of this phenomenon remain poorly understood. RESULTS Therefore, for the first time, a L-phenylalanine overproducing Escherichia coli quadruple reporter strain was established for monitoring of general stress response, growth behavior, oxygen limitation and product formation of single cells based on mTagBFP2, mEmerald, CyOFP1, and mCardinal2 expression measured by flow cytometry. This strain was applied for the fed-batch production of L-phenylalanine from glycerol and ammonia in a stirred-tank bioreactor at homogeneous conditions compared to the same process in a novel two-compartment bioreactor. This two-compartment bioreactor consists of a stirred-tank bioreactor with an initial volume of 0.9 L (homogeneous zone) with a coiled flow inverter with a fixed working volume of 0.45 L as a bypass (limitation zone) operated at a mean hydraulic residence time of 102 s. The product formation was similar in both bioreactor setups with maximum L-phenylalanine concentrations of 21.1 ± 0.6 g L-1 demonstrating the consistency of this study's microbial L-phenylalanine production. However, cell growth was vulnerable to repetitive exposure to the dynamically changing conditions in the two-compartment bioreactor with maximum biomass yields reduced by 21%. The functionality of reporter molecules was approved in the stirred-tank bioreactor cultivation, in which expressed fluorescence levels of all four markers were in accordance with respective process state variables. Additional evaluation of the distributions on single-cell level revealed the presence of population heterogeneity in both bioprocesses. Especially for the marker of the general stress response and the product formation, the corresponding histograms were characterized by bimodal shapes and broad distributions. These phenomena were pronounced particularly at the beginning and the end of the fed-batch process. CONCLUSIONS The here shown findings confirm multiple reporter strains to be a noninvasive tool for monitoring cellular characteristics and identifying potential subpopulations in bioprocesses. In combination with experiments in scale-down setups, these can be utilized for a better physiological understanding of bioprocesses and support future scale-up procedures.
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Affiliation(s)
- Manh Dat Hoang
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
| | - Ingmar Polte
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
| | - Lukas Frantzmann
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
| | - Nikolas von den Eichen
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
| | - Anna-Lena Heins
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany.
| | - Dirk Weuster-Botz
- Chair of Biochemical Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
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5
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Täuber S, Grünberger A. Microfluidic single-cell scale-down systems: introduction, application, and future challenges. Curr Opin Biotechnol 2023; 81:102915. [PMID: 36871470 DOI: 10.1016/j.copbio.2023.102915] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/17/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023]
Abstract
Performance losses during the scaling-up of bioprocesses from the laboratory to the production scale are common obstacles caused by the formation of concentration gradients in bioreactors. To overcome these obstacles, so-called scale-down bioreactors are used to analyze selected large-scale conditions and are one of the most important predictive tools for the successful transfer of bioprocesses from the lab to the industrial scale. In this regard, cellular behavior is usually measured as an averaged value, neglecting possible cell-to-cell heterogeneity within the culture. In contrast, microfluidic single-cell cultivation (MSCC) systems offer the possibility of understanding cellular processes on a single-cell level. To date, most MSCC systems have a limited choice of cultivation parameters that are not representative of bioprocess-relevant environmental conditions. Herein, we critically review recent advances in MSCC that allow the cultivation and analysis of cells under dynamic (bioprocess-relevant) environmental conditions. Finally, we discuss what technological advances and efforts are needed to bridge the gap between current MSCC systems and the use of these systems as single-cell scale-down devices.
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Affiliation(s)
- Sarah Täuber
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Bielefeld, Germany; Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Bielefeld, Germany; Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany; Microsystems in Bioprocess Engineering, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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6
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Mayer F, Cserjan-Puschmann M, Haslinger B, Shpylovyi A, Sam C, Soos M, Hahn R, Striedner G. Computational fluid dynamics simulation improves the design and characterization of a plug-flow-type scale-down reactor for microbial cultivation processes. Biotechnol J 2023; 18:e2200152. [PMID: 36442862 DOI: 10.1002/biot.202200152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/03/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022]
Abstract
The scale-up of bioprocesses remains one of the major obstacles in the biotechnology industry. Scale-down bioreactors have been identified as valuable tools to investigate the heterogeneities observed in large-scale tanks at the laboratory scale. Additionally, computational fluid dynamics (CFD) simulations can be used to gain information about fluid flow in tanks used for production. Here, we present the rational design and comprehensive characterization of a scale-down setup, in which a flexible and modular plug-flow reactor was connected to a stirred-tank bioreactor. With the help of CFD using the realizable k-ε model, the mixing time difference between a 20 and 4000 L bioreactor was evaluated and used as scale-down criterion. CFD simulations using a shear stress transport (SST) k-ω turbulence model were used to characterize the plug-flow reactor in more detail, and the model was verified using experiments. Additionally, the model was used to simulate conditions where experiments technically could not be performed due to sensor limitations. Nevertheless, verification is difficult in this case as well. This was the first time a scale-down setup was tested on high-cell-density Escherichia coli cultivations to produce industrially relevant antigen-binding fragments (Fab). Biomass yield was reduced by 11% and specific product yield was reduced by 20% during the scale-down cultivations. Additionally, the intracellular Fab fraction was increased by using the setup. The flexibility of the introduced scale-down setup in combination with CFD simulations makes it a valuable tool for investigating scale effects at the laboratory scale. More information about the large scale is still necessary to further refine the setup and to speed up bioprocess scale-up in the future.
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Affiliation(s)
- Florian Mayer
- Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Benedikt Haslinger
- Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Anton Shpylovyi
- Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christian Sam
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Miroslav Soos
- Department of Chemical Engineering, University of Chemistry and Technology Prague, Praha, Czech Republic
| | - Rainer Hahn
- Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gerald Striedner
- Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
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7
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Gutschmann B, Maldonado Simões M, Schiewe T, Schröter ES, Münzberg M, Neubauer P, Bockisch A, Riedel SL. Continuous feeding strategy for polyhydroxyalkanoate production from solid waste animal fat at laboratory- and pilot-scale. Microb Biotechnol 2022; 16:295-306. [PMID: 35921398 PMCID: PMC9871520 DOI: 10.1111/1751-7915.14104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/03/2022] [Accepted: 06/05/2022] [Indexed: 01/27/2023] Open
Abstract
Bioconversion of waste animal fat (WAF) to polyhydroxyalkanoates (PHAs) is an approach to lower the production costs of these plastic alternatives. However, the solid nature of WAF requires a tailor-made process development. In this study, a double-jacket feeding system was built to thermally liquefy the WAF to employ a continuous feeding strategy. During laboratory-scale cultivations with Ralstonia eutropha Re2058/pCB113, 70% more PHA (45 gPHA L-1 ) and a 75% higher space-time yield (0.63 gPHA L-1 h-1 ) were achieved compared to previously reported fermentations with solid WAF. During the development process, growth and PHA formation were monitored in real-time by in-line photon density wave spectroscopy. The process robustness was further evaluated during scale-down fermentations employing an oscillating aeration, which did not alter the PHA yield although cells encountered periods of oxygen limitation. Flow cytometry with propidium iodide staining showed that more than two-thirds of the cells were viable at the end of the cultivation and viability was even little higher in the scale-down cultivations. Application of this feeding system at 150-L pilot-scale cultivation yielded in 31.5 gPHA L-1 , which is a promising result for the further scale-up to industrial scale.
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Affiliation(s)
- Björn Gutschmann
- Technische Universität BerlinChair of Bioprocess EngineeringBerlinGermany
| | | | | | - Edith S. Schröter
- Technische Universität BerlinChair of Bioprocess EngineeringBerlinGermany
| | | | - Peter Neubauer
- Technische Universität BerlinChair of Bioprocess EngineeringBerlinGermany
| | - Anika Bockisch
- Technische Universität BerlinChair of Bioprocess EngineeringBerlinGermany,Bio‐PAT e.VBerlinGermany
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8
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Hartmann FSF, Udugama IA, Seibold GM, Sugiyama H, Gernaey KV. Digital models in biotechnology: Towards multi-scale integration and implementation. Biotechnol Adv 2022; 60:108015. [PMID: 35781047 DOI: 10.1016/j.biotechadv.2022.108015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/03/2022] [Accepted: 06/27/2022] [Indexed: 12/28/2022]
Abstract
Industrial biotechnology encompasses a large area of multi-scale and multi-disciplinary research activities. With the recent megatrend of digitalization sweeping across all industries, there is an increased focus in the biotechnology industry on developing, integrating and applying digital models to improve all aspects of industrial biotechnology. Given the rapid development of this field, we systematically classify the state-of-art modelling concepts applied at different scales in industrial biotechnology and critically discuss their current usage, advantages and limitations. Further, we critically analyzed current strategies to couple cell models with computational fluid dynamics to study the performance of industrial microorganisms in large-scale bioprocesses, which is of crucial importance for the bio-based production industries. One of the most challenging aspects in this context is gathering intracellular data under industrially relevant conditions. Towards comprehensive models, we discuss how different scale-down concepts combined with appropriate analytical tools can capture intracellular states of single cells. We finally illustrated how the efforts could be used to develop digitals models suitable for both cell factory design and process optimization at industrial scales in the future.
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Affiliation(s)
- Fabian S F Hartmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Isuru A Udugama
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, 113-8656 Tokyo, Japan; Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 228 A, 2800 Kgs. Lyngby, Denmark.
| | - Gerd M Seibold
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 223, 2800 Kgs. Lyngby, Denmark
| | - Hirokazu Sugiyama
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, 113-8656 Tokyo, Japan
| | - Krist V Gernaey
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 228 A, 2800 Kgs. Lyngby, Denmark.
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9
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Bernauer S, Eibl P, Witz C, Khinast J, Hardiman T. Analyzing the Effect of Using Axial Impellers in Large-Scale Bioreactors. Biotechnol Bioeng 2022; 119:2494-2504. [PMID: 35750654 DOI: 10.1002/bit.28163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/02/2022] [Accepted: 06/19/2022] [Indexed: 11/10/2022]
Abstract
In high-performance industrial fermentation processes, stirring and aeration may account for significant production costs. Compared to the widely applied Rushton impellers, axial-pumping impellers are known to yield a lower power draw and at the same time improve mixing. However, their lower gas dispersion capability requires stronger agitation, compromising these benefits. Diverse advanced impeller forms have been developed to cope with this challenge. We apply alternating radial and axial impellers and demonstrate strong gas dispersion and energy-efficient mixing for the first time in a large-scale (160 m3 ) bioreactor, based on experimental and CFD simulation data. For equal operating conditions (stirrer speed, aeration rate), this setup yielded similar gas hold-ups and better mixing times (35 %) compared to a classical Rushton-only configuration. Hence, applying a radial impeller on an upper level for improving gas dispersion maintains the benefits of axial impellers in terms of reducing energy demand (up to 50 %). We conclude that this effect is significant only at large-scale, when bubbles substantially expand due to the release of the hydrostatic pressure and have time to coalesce. The work thus extends current knowledge on mixing and aeration of large-scale reactors using classical impeller types. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sören Bernauer
- Sandoz GmbH, Novartis Technical Operations - Anti-Infectives, Process Development, Biochemiestrasse 10, 6250, Kundl, Austria
| | - Philipp Eibl
- Graz University of Technology, Institute for Process and Particle Engineering, Inffeldgasse 13, 8010, Graz, Austria.,SimVantage GmbH, Inffeldgasse 13, 8010, Graz, Austria
| | | | - Johannes Khinast
- Graz University of Technology, Institute for Process and Particle Engineering, Inffeldgasse 13, 8010, Graz, Austria
| | - Timo Hardiman
- Sandoz GmbH, Novartis Technical Operations - Anti-Infectives, Process Development, Biochemiestrasse 10, 6250, Kundl, Austria
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10
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Zakrzewski R, Lee K, Lye GJ. Development of a miniature bioreactor model to study the impact of pH and DOT fluctuations on CHO cell culture performance as a tool to understanding heterogeneity effects at large-scale. Biotechnol Prog 2022; 38:e3264. [PMID: 35441833 PMCID: PMC9542549 DOI: 10.1002/btpr.3264] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/07/2022] [Indexed: 12/04/2022]
Abstract
Understanding the impact of spatial heterogeneities that are known to occur in large‐scale cell culture bioreactors remains a significant challenge. This work presents a novel methodology for mimicking the effects of pH and dissolved oxygen heterogeneities on Chinese hamster ovary (CHO) cell culture performance and antibody quality characteristics, using an automated miniature bioreactor system. Cultures of 4 different cell lines, expressing 3 IgG molecules and one fusion protein, were exposed to repeated pH and dissolved oxygen tension (DOT) fluctuations between pH 7.0–7.5 and DOT 10%–30%, respectively, for durations of 15, 30, and 60 min. Fluctuations in pH had a minimal impact on growth, productivity, and product quality although some changes in lactate metabolism were observed. DOT fluctuations were found to have a more significant impact; a 35% decrease in cell growth and product titre was observed in the fastest growing cell line tested, while all cell lines exhibited a significant increase in lactate accumulation. Product quality analysis yielded varied results; two cell lines showed an increase in the G0F glycan and decrease in G1F, G2F, and Man5; however, another line showed the opposite trend. The study suggests that the response of CHO cells to the effects of fluctuating culture conditions is cell line specific and that higher growing cell lines are most impacted. The miniature bioreactor system described in this work therefore provides a platform for use during early stage cell culture process development to identify cell lines that may be adversely impacted by the pH and DOT heterogeneities encountered on scale‐up. This experimental data can be combined with computational modeling approaches to predict overall cell culture performance in large‐scale bioreactors.
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Affiliation(s)
- Roman Zakrzewski
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, London, UK
| | - Kenneth Lee
- Cell Culture and Fermentation Science, R&D, AstraZeneca, Franklin Building, Granta Park, Cambridge, UK
| | - Gary J Lye
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, London, UK
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11
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Janoska A, Verheijen JJ, Tang W, Lee Q, Sikkema B, van Gulik WM. Influence of oxygen concentration on the metabolism of Penicillium chrysogenum. Eng Life Sci 2022; 23:e2100139. [PMID: 36619886 PMCID: PMC9815084 DOI: 10.1002/elsc.202100139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/17/2022] [Accepted: 03/08/2022] [Indexed: 01/11/2023] Open
Abstract
In large-scale bioreactors, there is often insufficient mixing and as a consequence, cells experience uneven substrate and oxygen levels that influence product formation. In this study, the influence of dissolved oxygen (DO) gradients on the primary and secondary metabolism of a high producing industrial strain of Penicillium chrysogenum was investigated. Within a wide range of DO concentrations, obtained under chemostat conditions, we observed different responses from P. chrysogenum: (i) no influence on growth or penicillin production (>0.025 mmol L-1); (ii) reduced penicillin production, but no growth limitation (0.013-0.025 mmol L-1); and (iii) growth and penicillin production limitations (<0.013 mmol L-1). In addition, scale down experiments were performed by oscillating the DO concentration in the bioreactor. We found that during DO oscillation, the penicillin production rate decreased below the value observed when a constant DO equal to the average oscillating DO value was used. To understand and predict the influence of oxygen levels on primary metabolism and penicillin production, we developed a black box model that was linked to a detailed kinetic model of the penicillin pathway. The model simulations represented the experimental data during the step experiments; however, during the oscillation experiments the predictions deviated, indicating the involvement of the central metabolism in penicillin production.
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Affiliation(s)
- Agnes Janoska
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Jelle J. Verheijen
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Wenjung Tang
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands,DSM Biotechnology CenterAlexander Fleminglaan 1DelftNetherlands
| | - Queenie Lee
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Baukje Sikkema
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Walter M. van Gulik
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
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12
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Ho P, Täuber S, Stute B, Grünberger A, von Lieres E. Microfluidic Reproduction of Dynamic Bioreactor Environment Based on Computational Lifelines. FRONTIERS IN CHEMICAL ENGINEERING 2022. [DOI: 10.3389/fceng.2022.826485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The biotechnological production of fine chemicals, proteins and pharmaceuticals is usually hampered by loss of microbial performance during scale-up. This challenge is mainly caused by discrepancies between homogeneous environmental conditions at laboratory scale, where bioprocesses are optimized, and inhomogeneous conditions in large-scale bioreactors, where production takes place. Therefore, to improve strain selection and process development, it is of great interest to characterize these fluctuating conditions at large-scale and to study their effects on microbial cells. In this paper, we demonstrate the potential of computational fluid dynamics (CFD) simulation of large-scale bioreactors combined with dynamic microfluidic single-cell cultivation (dMSCC). Environmental conditions in a 200 L bioreactor were characterized with CFD simulations. Computational lifelines were determined by combining simulated turbulent multiphase flow, mass transport and particle tracing. Glucose availability for Corynebacterium glutamicum cells was determined. The reactor was simulated with average glucose concentrations of 6 g m−3, 10 g m−3 and 16 g m−3. The resulting computational lifelines, discretized into starvation and abundance regimes, were used as feed profiles for the dMSCC to investigate how varying glucose concentration affects cell physiology and growth rate. In this study, each colony in the dMSCC device represents a single cell as it travels through the reactor. Under oscillating conditions reproduced in the dMSCC device, a decrease in growth rate of about 40% was observed compared to continuous supply with the same average glucose availability. The presented approach provides insights into environmental conditions observed by microorganisms in large-scale bioreactors. It also paves the way for an improved understanding of how inhomogeneous environmental conditions influence cellular physiology, growth and production.
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Minden S, Aniolek M, Sarkizi Shams Hajian C, Teleki A, Zerrer T, Delvigne F, van Gulik W, Deshmukh A, Noorman H, Takors R. Monitoring Intracellular Metabolite Dynamics in Saccharomyces cerevisiae during Industrially Relevant Famine Stimuli. Metabolites 2022; 12:metabo12030263. [PMID: 35323706 PMCID: PMC8953226 DOI: 10.3390/metabo12030263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 11/16/2022] Open
Abstract
Carbon limitation is a common feeding strategy in bioprocesses to enable an efficient microbiological conversion of a substrate to a product. However, industrial settings inherently promote mixing insufficiencies, creating zones of famine conditions. Cells frequently traveling through such regions repeatedly experience substrate shortages and respond individually but often with a deteriorated production performance. A priori knowledge of the expected strain performance would enable targeted strain, process, and bioreactor engineering for minimizing performance loss. Today, computational fluid dynamics (CFD) coupled to data-driven kinetic models are a promising route for the in silico investigation of the impact of the dynamic environment in the large-scale bioreactor on microbial performance. However, profound wet-lab datasets are needed to cover relevant perturbations on realistic time scales. As a pioneering study, we quantified intracellular metabolome dynamics of Saccharomyces cerevisiae following an industrially relevant famine perturbation. Stimulus-response experiments were operated as chemostats with an intermittent feed and high-frequency sampling. Our results reveal that even mild glucose gradients in the range of 100 µmol·L−1 impose significant perturbations in adapted and non-adapted yeast cells, altering energy and redox homeostasis. Apparently, yeast sacrifices catabolic reduction charges for the sake of anabolic persistence under acute carbon starvation conditions. After repeated exposure to famine conditions, adapted cells show 2.7% increased maintenance demands.
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Affiliation(s)
- Steven Minden
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Maria Aniolek
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Christopher Sarkizi Shams Hajian
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Tobias Zerrer
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Frank Delvigne
- Microbial Processes and Interactions (MiPI), TERRA Research and Teaching Centre, Gembloux Agro Bio Tech, University of Liege, 5030 Gembloux, Belgium;
| | - Walter van Gulik
- Department of Biotechnology, Delft University of Technology, van der Maasweg 6, 2629 HZ Delft, The Netherlands;
| | - Amit Deshmukh
- Royal DSM, 2613 AX Delft, The Netherlands; (A.D.); (H.N.)
| | - Henk Noorman
- Royal DSM, 2613 AX Delft, The Netherlands; (A.D.); (H.N.)
- Department of Biotechnology, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
- Correspondence:
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Gaugler L, Mast Y, Fitschen J, Hofmann S, Schlüter M, Takors R. Scaling-down biopharmaceutical production processes via a single multi-compartment bioreactor (SMCB). Eng Life Sci 2022; 23:e2100161. [PMID: 36619888 PMCID: PMC9815078 DOI: 10.1002/elsc.202100161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 01/11/2023] Open
Abstract
Biopharmaceutical production processes often use mammalian cells in bioreactors larger than 10,000 L, where gradients of shear stress, substrate, dissolved oxygen and carbon dioxide, and pH are likely to occur. As former tissue cells, producer cell lines such as Chinese hamster ovary (CHO) cells sensitively respond to these mixing heterogeneities, resulting in related scenarios being mimicked in scale-down reactors. However, commonly applied multi-compartment approaches comprising multiple reactors impose a biasing shear stress caused by pumping. The latter can be prevented using the single multi-compartment bioreactor (SMCB) presented here. The exchange area provided by a disc mounted between the upper and lower compartments in a stirred bioreactor was found to be an essential design parameter. Mimicking the mixing power input at a large scale on a small scale allowed the installation of similar mixing times in the SMCB. The particularities of the disc geometry may also be considered, finally leading to a converged decision tree. The work flow identifies a sharply contoured operational field comprising disc designs and power input to install the same mixing times on a large scale in the SMCB without the additional shear stress caused by pumping. The design principle holds true for both nongassed and gassed systems.
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Affiliation(s)
- Lena Gaugler
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Yannic Mast
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Jürgen Fitschen
- Institute of Multiphase FlowsHamburg University of TechnologyHamburgGermany
| | - Sebastian Hofmann
- Institute of Multiphase FlowsHamburg University of TechnologyHamburgGermany
| | - Michael Schlüter
- Institute of Multiphase FlowsHamburg University of TechnologyHamburgGermany
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
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Vivek V, Eka FN, Chew W. Mixing studies in an unbaffled bioreactor using a computational model corroborated with in-situ Raman and imaging analyses. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2021.100232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Bayer B, Duerkop M, Striedner G, Sissolak B. Model Transferability and Reduced Experimental Burden in Cell Culture Process Development Facilitated by Hybrid Modeling and Intensified Design of Experiments. Front Bioeng Biotechnol 2022; 9:740215. [PMID: 35004635 PMCID: PMC8733703 DOI: 10.3389/fbioe.2021.740215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/22/2021] [Indexed: 12/22/2022] Open
Abstract
Reliable process development is accompanied by intense experimental effort. The utilization of an intensified design of experiments (iDoE) (intra-experimental critical process parameter (CPP) shifts combined) with hybrid modeling potentially reduces process development burden. The iDoE can provide more process response information in less overall process time, whereas hybrid modeling serves as a commodity to describe this behavior the best way. Therefore, a combination of both approaches appears beneficial for faster design screening and is especially of interest at larger scales where the costs per experiment rise significantly. Ideally, profound process knowledge is gathered at a small scale and only complemented with few validation experiments on a larger scale, saving valuable resources. In this work, the transferability of hybrid modeling for Chinese hamster ovary cell bioprocess development along process scales was investigated. A two-dimensional DoE was fully characterized in shake flask duplicates (300 ml), containing three different levels for the cultivation temperature and the glucose concentration in the feed. Based on these data, a hybrid model was developed, and its performance was assessed by estimating the viable cell concentration and product titer in 15 L bioprocesses with the same DoE settings. To challenge the modeling approach, 15 L bioprocesses also comprised iDoE runs with intra-experimental CPP shifts, impacting specific cell rates such as growth, consumption, and formation. Subsequently, the applicability of the iDoE cultivations to estimate static cultivations was also investigated. The shaker-scale hybrid model proved suitable for application to a 15 L scale (1:50), estimating the viable cell concentration and the product titer with an NRMSE of 10.92% and 17.79%, respectively. Additionally, the iDoE hybrid model performed comparably, displaying NRMSE values of 13.75% and 21.13%. The low errors when transferring the models from shaker to reactor and between the DoE and the iDoE approach highlight the suitability of hybrid modeling for mammalian cell culture bioprocess development and the potential of iDoE to accelerate process characterization and to improve process understanding.
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Affiliation(s)
- Benjamin Bayer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Novasign GmbH, Vienna, Austria
| | - Mark Duerkop
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Novasign GmbH, Vienna, Austria
| | - Gerald Striedner
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Novasign GmbH, Vienna, Austria
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Yang Q, Lin W, Xu J, Guo N, Zhao J, Wang G, Wang Y, Chu J, Wang G. Changes in Oxygen Availability during Glucose-Limited Chemostat Cultivations of Penicillium chrysogenum Lead to Rapid Metabolite, Flux and Productivity Responses. Metabolites 2022; 12:metabo12010045. [PMID: 35050169 PMCID: PMC8780904 DOI: 10.3390/metabo12010045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/02/2022] [Accepted: 01/03/2022] [Indexed: 02/01/2023] Open
Abstract
Bioreactor scale-up from the laboratory scale to the industrial scale has always been a pivotal step in bioprocess development. However, the transition of a bioeconomy from innovation to commercialization is often hampered by performance loss in titer, rate and yield. These are often ascribed to temporal variations of substrate and dissolved oxygen (for instance) in the environment, experienced by microorganisms at the industrial scale. Oscillations in dissolved oxygen (DO) concentration are not uncommon. Furthermore, these fluctuations can be exacerbated with poor mixing and mass transfer limitations, especially in fermentations with filamentous fungus as the microbial cell factory. In this work, the response of glucose-limited chemostat cultures of an industrial Penicillium chrysogenum strain to different dissolved oxygen levels was assessed under both DO shift-down (60% → 20%, 10% and 5%) and DO ramp-down (60% → 0% in 24 h) conditions. Collectively, the results revealed that the penicillin productivity decreased as the DO level dropped down below 20%, while the byproducts, e.g., 6-oxopiperidine-2-carboxylic acid (OPC) and 6-aminopenicillanic acid (6APA), accumulated. Following DO ramp-down, penicillin productivity under DO shift-up experiments returned to its maximum value in 60 h when the DO was reset to 60%. The result showed that a higher cytosolic redox status, indicated by NADH/NAD+, was observed in the presence of insufficient oxygen supply. Consistent with this, flux balance analysis indicated that the flux through the glyoxylate shunt was increased by a factor of 50 at a DO value of 5% compared to the reference control, favoring the maintenance of redox status. Interestingly, it was observed that, in comparison with the reference control, the penicillin productivity was reduced by 25% at a DO value of 5% under steady state conditions. Only a 14% reduction in penicillin productivity was observed as the DO level was ramped down to 0. Furthermore, intracellular levels of amino acids were less sensitive to DO levels at DO shift-down relative to DO ramp-down conditions; this difference could be caused by different timescales between turnover rates of amino acid pools (tens of seconds to minutes) and DO switches (hours to days at steady state and minutes to hours at ramp-down). In summary, this study showed that changes in oxygen availability can lead to rapid metabolite, flux and productivity responses, and dynamic DO perturbations could provide insight into understanding of metabolic responses in large-scale bioreactors.
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Benalcázar EA, Noorman H, Filho RM, Posada JA. Decarbonizing ethanol production via gas fermentation: impact of the CO/H2/CO2 mix source on greenhouse gas emissions and production costs. Comput Chem Eng 2022. [DOI: 10.1016/j.compchemeng.2022.107670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Sadino‐Riquelme MC, Rivas J, Jeison D, Donoso‐Bravo A, Hayes RE. Computational modelling of mixing tanks for bioprocesses: Developing a comprehensive workflow. CAN J CHEM ENG 2021. [DOI: 10.1002/cjce.24220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - José Rivas
- Departamento de Ingeniería Química y Ambiental Universidad Técnica Federico Santa María Santiago Chile
| | - David Jeison
- Escuela de Ingeniería Bioquímica Pontificia Universidad Católica de Valparaíso Valparaíso Chile
| | - Andrés Donoso‐Bravo
- Departamento de Ingeniería Química y Ambiental Universidad Técnica Federico Santa María Santiago Chile
- CETAQUA Centro Tecnológico del Agua Las Condes Chile
| | - Robert E. Hayes
- Department of Chemical and Materials Engineering University of Alberta Edmonton Alberta Canada
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Ziegler M, Zieringer J, Döring CL, Paul L, Schaal C, Takors R. Engineering of a robust Escherichia coli chassis and exploitation for large-scale production processes. Metab Eng 2021; 67:75-87. [PMID: 34098100 DOI: 10.1016/j.ymben.2021.05.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 11/28/2022]
Abstract
In large-scale bioprocesses microbes are exposed to heterogeneous substrate availability reducing the overall process performance. A series of deletion strains was constructed from E. coli MG1655 aiming for a robust phenotype in heterogeneous fermentations with transient starvation. Deletion targets were hand-picked based on a list of genes derived from previous large-scale simulation runs. Each gene deletion was conducted on the premise of strict neutrality towards growth parameters in glucose minimal medium. The final strain of the series, named E. coli RM214, was cultivated continuously in an STR-PFR (stirred tank reactor - plug flow reactor) scale-down reactor. The scale-down reactor system simulated repeated passages through a glucose starvation zone. When exposed to nutrient gradients, E. coli RM214 had a significantly lower maintenance coefficient than E. coli MG1655 (Δms = 0.038 gGlucose/gCDW/h, p < 0.05). In an exemplary protein production scenario E. coli RM214 remained significantly more productive than E. coli MG1655 reaching 44% higher eGFP yield after 28 h of STR-PFR cultivation. This study developed E. coli RM214 as a robust chassis strain and demonstrated the feasibility of engineering microbial hosts for large-scale applications.
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Affiliation(s)
- Martin Ziegler
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Julia Zieringer
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Clarissa-Laura Döring
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Liv Paul
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Christoph Schaal
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
| | - Ralf Takors
- University of Stuttgart - Institute of Biochemical Engineering, Allmandring 31, 70569, Stuttgart, Germany.
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Ziegler M, Zieringer J, Takors R. Transcriptional profiling of the stringent response mutant strain E. coli SR reveals enhanced robustness to large-scale conditions. Microb Biotechnol 2021; 14:993-1010. [PMID: 33369128 PMCID: PMC8085953 DOI: 10.1111/1751-7915.13738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/05/2022] Open
Abstract
In large-scale fed-batch production processes, microbes are exposed to heterogeneous substrate availability caused by long mixing times. Escherichia coli, the most common industrial host for recombinant protein production, reacts by recurring accumulation of the alarmone ppGpp and energetically wasteful transcriptional strategies. Here, we compare the regulatory responses of the stringent response mutant strain E. coli SR and its parent strain E. coli MG1655 to repeated nutrient starvation in a two-compartment scale-down reactor. Our data show that E. coli SR can withstand these stress conditions without a ppGpp-mediated stress response maintaining fully functional ammonium uptake and biomass formation. Furthermore, E. coli SR exhibited a substantially reduced short-term transcriptional response compared to E. coli MG1655 (less than half as many differentially expressed genes). E. coli SR proceeded adaptation via more general SOS response pathways by initiating negative regulation of transcription, translation and cell division. Our results show that locally induced stress responses propagating through the bioreactor do not result in cyclical induction and repression of genes in E. coli SR, but in a reduced and coordinated response, which makes it potentially suitable for large-scale production processes.
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Affiliation(s)
- Martin Ziegler
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Julia Zieringer
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
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Euler-Lagrangian Simulations: A Proper Tool for Predicting Cellular Performance in Industrial Scale Bioreactors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021. [PMID: 32978650 DOI: 10.1007/10_2020_133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Eulerian-Lagrangian approach to investigate cellular responses in a bioreactor has become the center of attention in recent years. It was introduced to biotechnological processes about two decades ago, but within the last few years, it proved itself as a powerful tool to address scale-up and -down topics of bioprocesses. It can capture the history of a cell and reveal invaluable information for, not only, bioprocess control and design but also strain engineering. This way it will be possible to shed light on the actual environment that cell experiences throughout its lifespan. Lifelines of a microorganism in a bioreactor can serve as the missing link that encompasses the biological timescales and the physical timescales. For this purpose digitalization of bioreactors provides us with new insights that are not achievable in industrial reactors easily if at all, namely, substrate and product gradients; high-shear regions are among the most interesting factors that can be reproduced adequately with help of a digital twin. In this chapter basic principles of this method will be introduced, and later on some practical aspects of particle tracking technique will be illustrated. In the final section, some of the advantages and challenges associated with this method will be discussed.
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Xia J, Wang G, Fan M, Chen M, Wang Z, Zhuang Y. Understanding the scale-up of fermentation processes from the viewpoint of the flow field in bioreactors and the physiological response of strains. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Potential of Integrating Model-Based Design of Experiments Approaches and Process Analytical Technologies for Bioprocess Scale-Down. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021. [PMID: 33381857 DOI: 10.1007/10_2020_154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Typically, bioprocesses on an industrial scale are dynamic systems with a certain degree of variability, system inhomogeneities, and even population heterogeneities. Therefore, the scaling of such processes from laboratory to industrial scale and vice versa is not a trivial task. Traditional scale-down methodologies consider several technical parameters, so that systems on the laboratory scale tend to qualitatively reflect large-scale effects, but not the dynamic situation in an industrial bioreactor over the entire process, from the perspective of a cell. Supported by the enormous increase in computing power, the latest scientific focus is on the application of dynamic models, in combination with computational fluid dynamics to quantitatively describe cell behavior. These models allow the description of possible cellular lifelines which in turn can be used to derive a regime analysis for scale-down experiments. However, the approaches described so far, which were for a very few process examples, are very labor- and time-intensive and cannot be validated easily. In parallel, alternatives have been developed based on the description of the industrial process with hybrid process models, which describe a process mechanistically as far as possible in order to determine the essential process parameters with their respective variances. On-line analytical methods allow the characterization of population heterogeneity directly in the process. This detailed information from the industrial process can be used in laboratory screening systems to select relevant conditions in which the cell and process related parameters reflect the situation in the industrial scale. In our opinion, these technologies, which are available in research for modeling biological systems, in combination with process analytical techniques are so far developed that they can be implemented in industrial routines for faster development of new processes and optimization of existing ones.
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Predicting By-Product Gradients of Baker’s Yeast Production at Industrial Scale: A Practical Simulation Approach. Processes (Basel) 2020. [DOI: 10.3390/pr8121554] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Scaling up bioprocesses is one of the most crucial steps in the commercialization of bioproducts. While it is known that concentration and shear rate gradients occur at larger scales, it is often too risky, if feasible at all, to conduct validation experiments at such scales. Using computational fluid dynamics equipped with mechanistic biochemical engineering knowledge of the process, it is possible to simulate such gradients. In this work, concentration profiles for the by-products of baker’s yeast production are investigated. By applying a mechanistic black-box model, concentration heterogeneities for oxygen, glucose, ethanol, and carbon dioxide are evaluated. The results suggest that, although at low concentrations, ethanol is consumed in more than 90% of the tank volume, which prevents cell starvation, even when glucose is virtually depleted. Moreover, long exposure to high dissolved carbon dioxide levels is predicted. Two biomass concentrations, i.e., 10 and 25 g/L, are considered where, in the former, ethanol production is solely because of overflow metabolism while, in the latter, 10% of the ethanol formation is due to dissolved oxygen limitation. This method facilitates the prediction of the living conditions of the microorganism and its utilization to address the limitations via change of strain or bioreactor design or operation conditions. The outcome can also be of value to design a representative scale-down reactor to facilitate strain studies.
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Understanding gradients in industrial bioreactors. Biotechnol Adv 2020; 46:107660. [PMID: 33221379 DOI: 10.1016/j.biotechadv.2020.107660] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/22/2020] [Accepted: 11/14/2020] [Indexed: 01/07/2023]
Abstract
Gradients in industrial bioreactors have attracted substantial research attention since exposure to fluctuating environmental conditions has been shown to lead to changes in the metabolome, transcriptome as well as population heterogeneity in industrially relevant microorganisms. Such changes have also been found to impact key process parameters like the yield on substrate and the productivity. Hence, understanding gradients is important from both the academic and industrial perspectives. In this review the causes of gradients are outlined, along with their impact on microbial physiology. Quantifying the impact of gradients requires a detailed understanding of both fluid flow inside industrial equipment and microbial physiology. This review critically examines approaches used to investigate gradients including large-scale experimental work, computational methods and scale-down approaches. Avenues for future work have been highlighted, particularly the need for further coordinated development of both in silico and experimental tools which can be used to further the current understanding of gradients in industrial equipment.
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Bisgaard J, Muldbak M, Cornelissen S, Tajsoleiman T, Huusom JK, Rasmussen T, Gernaey KV. Flow-following sensor devices: A tool for bridging data and model predictions in large-scale fermentations. Comput Struct Biotechnol J 2020; 18:2908-2919. [PMID: 33163151 PMCID: PMC7595931 DOI: 10.1016/j.csbj.2020.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/27/2020] [Accepted: 10/02/2020] [Indexed: 12/11/2022] Open
Abstract
Production-scale fermentation processes in industrial biotechnology experience gradients in process variables, such as dissolved gases, pH and substrate concentrations, which can potentially affect the production organism and therefore the yield and profitability of the processes. However, the extent of the heterogeneity is unclear, as it is currently a challenge at large scale to obtain representative measurements from different zones of the reactor volume. Computational fluid dynamics (CFD) models have proven to be a valuable tool for better understanding the environment inside bioreactors. Without detailed measurements to support the CFD predictions, the validity of CFD models is debatable. A promising technology to obtain such measurements from different zones in the bioreactors are flow-following sensor devices, whose development has recently benefitted from advancements in microelectronics and sensor technology. This paper presents the state of the art within flow-following sensor device technology and addresses how the technology can be used in large-scale bioreactors to improve the understanding of the process itself and to test the validity of detailed computational models of the bioreactors in the future.
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Affiliation(s)
- Jonas Bisgaard
- Freesense ApS, Copenhagen, Denmark.,Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 228A, 2800 Kgs. Lyngby, Denmark
| | - Monica Muldbak
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 228A, 2800 Kgs. Lyngby, Denmark
| | | | - Tannaz Tajsoleiman
- Freesense ApS, Copenhagen, Denmark.,Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 228A, 2800 Kgs. Lyngby, Denmark
| | - Jakob K Huusom
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 228A, 2800 Kgs. Lyngby, Denmark
| | | | - Krist V Gernaey
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 228A, 2800 Kgs. Lyngby, Denmark
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Zieringer J, Wild M, Takors R. Data-driven in silico prediction of regulation heterogeneity and ATP demands of Escherichia coli in large-scale bioreactors. Biotechnol Bioeng 2020; 118:265-278. [PMID: 32940924 DOI: 10.1002/bit.27568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/11/2020] [Accepted: 09/11/2020] [Indexed: 12/31/2022]
Abstract
Escherichia coli exposed to industrial-scale heterogeneous mixing conditions respond to external stress by initiating short-term metabolic and long-term strategic transcriptional programs. In native habitats, long-term strategies allow survival in severe stress but are of limited use in large bioreactors, where microenvironmental conditions may change right after said programs are started. Related on/off switching of genes causes additional ATP burden that may reduce the cellular capacity for producing the desired product. Here, we present an agent-based data-driven model linked to computational fluid dynamics, finally allowing to predict additional ATP needs of Escherichia coli K12 W3110 exposed to realistic large-scale bioreactor conditions. The complex model describes transcriptional up- and downregulation dynamics of about 600 genes starting from subminute range covering 28 h. The data-based approach was extracted from comprehensive scale-down experiments. Simulating mixing and mass transfer conditions in a 54 m3 stirred bioreactor, 120,000 E. coli cells were tracked while fluctuating between different zones of glucose availability. It was found that cellular ATP demands rise between 30% and 45% of growth decoupled maintenance needs, which may limit the production of ATP-intensive product formation accordingly. Furthermore, spatial analysis of individual cell transcriptional patterns reveal very heterogeneous gene amplifications with hot spots of 50%-80% messenger RNA upregulation in the upper region of the bioreactor. The phenomenon reflects the time-delayed regulatory response of the cells that propagate through the stirred tank. After 4.2 h, cells adapt to environmental changes but still have to bear an additional 6% ATP demand.
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Affiliation(s)
- Julia Zieringer
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Moritz Wild
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
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Wang G, Haringa C, Noorman H, Chu J, Zhuang Y. Developing a Computational Framework To Advance Bioprocess Scale-Up. Trends Biotechnol 2020; 38:846-856. [DOI: 10.1016/j.tibtech.2020.01.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 01/10/2023]
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Paul K, Böttinger K, Mitic BM, Scherfler G, Posch C, Behrens D, Huber CG, Herwig C. Development, characterization, and application of a 2-Compartment system to investigate the impact of pH inhomogeneities in large-scale CHO-based processes. Eng Life Sci 2020; 20:368-378. [PMID: 32774209 PMCID: PMC7401239 DOI: 10.1002/elsc.202000009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/08/2020] [Accepted: 04/29/2020] [Indexed: 01/05/2023] Open
Abstract
Large-scale bioreactors for the production of monoclonal antibodies reach volumes of up to 25 000 L. With increasing bioreactor size, mixing is however affected negatively, resulting in the formation of gradients throughout the reactor. These gradients can adversely affect process performance at large scale. Since mammalian cells are sensitive to changes in pH, this study investigated the effects of pH gradients on process performance. A 2-Compartment System was established for this purpose to expose only a fraction of the cell population to pH excursions and thereby mimicking a large-scale bioreactor. Cells were exposed to repeated pH amplitudes of 0.4 units (pH 7.3), which resulted in decreased viable cell counts, as well as the inhibition of the lactate metabolic shift. These effects were furthermore accompanied by increased absolute lactate levels. Continuous assessment of molecular attributes of the expressed target protein revealed that subunit assembly or N-glycosylation patterns were only slightly influenced by the pH excursions. The exposure of more cells to the same pH amplitudes further impaired process performance, indicating this is an important factor, which influences the impact of pH inhomogeneity. This knowledge can aid in the design of pH control strategies to minimize the effects of pH inhomogeneity in large-scale bioreactors.
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Affiliation(s)
- Katrin Paul
- Institute of ChemicalEnvironmental and Bioscience EngineeringTU WienViennaAustria
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved BioprocessesTU WienViennaAustria
| | - Katharina Böttinger
- Department of BiosciencesBioanalytical Research LabsUniversity of SalzburgSalzburgAustria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar CharacterizationUniversity of SalzburgSalzburgAustria
| | - Bernd M. Mitic
- Institute of ChemicalEnvironmental and Bioscience EngineeringTU WienViennaAustria
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved BioprocessesTU WienViennaAustria
| | - Georg Scherfler
- Institute of ChemicalEnvironmental and Bioscience EngineeringTU WienViennaAustria
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved BioprocessesTU WienViennaAustria
| | | | | | - Christian G. Huber
- Department of BiosciencesBioanalytical Research LabsUniversity of SalzburgSalzburgAustria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar CharacterizationUniversity of SalzburgSalzburgAustria
| | - Christoph Herwig
- Institute of ChemicalEnvironmental and Bioscience EngineeringTU WienViennaAustria
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved BioprocessesTU WienViennaAustria
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Holguín-Salas A, Corkidi G, Galindo E. Local bubble size distribution in a pilot scale stirred tank containing a mycelial (three phases) dispersion as a function of constant retrofitted gassed power input. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Vasilakou E, van Loosdrecht MCM, Wahl SA. Escherichia coli metabolism under short-term repetitive substrate dynamics: adaptation and trade-offs. Microb Cell Fact 2020; 19:116. [PMID: 32471427 PMCID: PMC7260802 DOI: 10.1186/s12934-020-01379-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/25/2020] [Indexed: 12/04/2022] Open
Abstract
Background Microbial metabolism is highly dependent on the environmental conditions. Especially, the substrate concentration, as well as oxygen availability, determine the metabolic rates. In large-scale bioreactors, microorganisms encounter dynamic conditions in substrate and oxygen availability (mixing limitations), which influence their metabolism and subsequently their physiology. Earlier, single substrate pulse experiments were not able to explain the observed physiological changes generated under large-scale industrial fermentation conditions. Results In this study we applied a repetitive feast–famine regime in an aerobic Escherichia coli culture in a time-scale of seconds. The regime was applied for several generations, allowing cells to adapt to the (repetitive) dynamic environment. The observed response was highly reproducible over the cycles, indicating that cells were indeed fully adapted to the regime. We observed an increase of the specific substrate and oxygen consumption (average) rates during the feast–famine regime, compared to a steady-state (chemostat) reference environment. The increased rates at same (average) growth rate led to a reduced biomass yield (30% lower). Interestingly, this drop was not followed by increased by-product formation, pointing to the existence of energy-spilling reactions. During the feast–famine cycle, the cells rapidly increased their uptake rate. Within 10 s after the beginning of the feeding, the substrate uptake rate was higher (4.68 μmol/gCDW/s) than reported during batch growth (3.3 μmol/gCDW/s). The high uptake led to an accumulation of several intracellular metabolites, during the feast phase, accounting for up to 34% of the carbon supplied. Although the metabolite concentrations changed rapidly, the cellular energy charge remained unaffected, suggesting well-controlled balance between ATP producing and ATP consuming reactions. Conclusions The adaptation of the physiology and metabolism of E. coli under substrate dynamics, representative for large-scale fermenters, revealed the existence of several cellular mechanisms coping with stress. Changes in the substrate uptake system, storage potential and energy-spilling processes resulted to be of great importance. These metabolic strategies consist a meaningful step to further tackle reduced microbial performance, observed under large-scale cultivations.
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Affiliation(s)
- Eleni Vasilakou
- Department of Biotechnology, Delft University of Technology, Van der Maasweg, 2629 HZ, Delft, The Netherlands.
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van der Maasweg, 2629 HZ, Delft, The Netherlands
| | - S Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Van der Maasweg, 2629 HZ, Delft, The Netherlands.
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Olughu W, Nienow A, Hewitt C, Rielly C. Scale-down studies for the scale-up of a recombinant Corynebacterium glutamicum fed-batch fermentation: loss of homogeneity leads to lower levels of cadaverine production. JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY (OXFORD, OXFORDSHIRE : 1986) 2020; 95:675-685. [PMID: 32139953 PMCID: PMC7043379 DOI: 10.1002/jctb.6248] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 09/30/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND The loss of efficiency and performance of bioprocesses on scale-up is well known, but not fully understood. This work addresses this problem, by studying the effect of some fermentation gradients (pH, glucose and oxygen) that occur at the larger scale in a bench-scale two-compartment reactor [plug flow reactor (PFR) + stirred tank reactor (STR)] using the cadaverine-producing recombinant Corynebacterium glutamicum DM1945 Δact3 Ptuf-ldcC_OPT. The new scale-down strategy developed here studied the effect of increasing the magnitude of fermentation gradients by considering not only the average cell residence time in the PFR (τ PFR), but also the mean frequency at which the bacterial cells entered the PFR (f m) section of the two-compartment reactor. RESULTS On implementing this strategy the cadaverine production decreased on average by 26%, 49% and 59% when the τ PFR was increased from 1 to 2 min and then 5 min respectively compared to the control fermentation. The carbon dioxide productivity was highest (3.1-fold that of the control) at a τ PFR of 5 min, but no losses were observed in biomass production. However, the population of viable but non-culturable cells increased as the magnitude of fermentation gradients was increased. The new scale-down approach was also shown to have a bigger impact on fermentation performance than the traditional one. CONCLUSION This study demonstrated that C. glutamicum DM1945 Δact3 Ptuf-ldcC_OPT physiological response was a function of the magnitude of fermentation gradients simulated. The adaptations of a bacterial cell within a heterogeneous environment ultimately result in losses in fermentation productivity as observed here. © 2019 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Williams Olughu
- Department of Chemical EngineeringLoughborough UniversityLoughboroughUK
- Ipsen Biopharma LtdWrexhamUK
| | - Alvin Nienow
- Department of Chemical EngineeringLoughborough UniversityLoughboroughUK
- School of Chemical EngineeringUniversity of BirminghamBirminghamUK
- School of Life and Health SciencesAston UniversityBirminghamUK
| | - Chris Hewitt
- School of Life and Health SciencesAston UniversityBirminghamUK
| | - Chris Rielly
- Department of Chemical EngineeringLoughborough UniversityLoughboroughUK
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Almeida Benalcázar E, Noorman H, Maciel Filho R, Posada JA. Modeling ethanol production through gas fermentation: a biothermodynamics and mass transfer-based hybrid model for microbial growth in a large-scale bubble column bioreactor. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:59. [PMID: 32231709 PMCID: PMC7102449 DOI: 10.1186/s13068-020-01695-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 03/05/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Ethanol production through fermentation of gas mixtures containing CO, CO2 and H2 has just started operating at commercial scale. However, quantitative schemes for understanding and predicting productivities, yields, mass transfer rates, gas flow profiles and detailed energy requirements have been lacking in literature; such are invaluable tools for process improvements and better systems design. The present study describes the construction of a hybrid model for simulating ethanol production inside a 700 m3 bubble column bioreactor fed with gas of two possible compositions, i.e., pure CO and a 3:1 mixture of H2 and CO2. RESULTS Estimations made using the thermodynamics-based black-box model of microbial reactions on substrate threshold concentrations, biomass yields, as well as CO and H2 maximum specific uptake rates agreed reasonably well with data and observations reported in literature. According to the bioreactor simulation, there is a strong dependency of process performance on mass transfer rates. When mass transfer coefficients were estimated using a model developed from oxygen transfer to water, ethanol productivity reached 5.1 g L-1 h-1; when the H2/CO2 mixture is fed to the bioreactor, productivity of CO fermentation was 19% lower. Gas utilization reached 23 and 17% for H2/CO2 and CO fermentations, respectively. If mass transfer coefficients were 100% higher than those estimated, ethanol productivity and gas utilization may reach 9.4 g L-1 h-1 and 38% when feeding the H2/CO2 mixture at the same process conditions. The largest energetic requirements for a complete manufacturing plant were identified for gas compression and ethanol distillation, being higher for CO fermentation due to the production of CO2. CONCLUSIONS The thermodynamics-based black-box model of microbial reactions may be used to quantitatively assess and consolidate the diversity of reported data on CO, CO2 and H2 threshold concentrations, biomass yields, maximum substrate uptake rates, and half-saturation constants for CO and H2 for syngas fermentations by acetogenic bacteria. The maximization of ethanol productivity in the bioreactor may come with a cost: low gas utilization. Exploiting the model flexibility, multi-objective optimizations of bioreactor performance might reveal how process conditions and configurations could be adjusted to guide further process development.
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Affiliation(s)
- Eduardo Almeida Benalcázar
- Department of Product and Process Development, Faculty of Chemical Engineering, State University of Campinas, Av. Albert Einstein 500, Cidade Universitária, Campinas, SP 13083-852 Brazil
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Henk Noorman
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
- DSM Biotechnology Center, A. Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Rubens Maciel Filho
- Department of Product and Process Development, Faculty of Chemical Engineering, State University of Campinas, Av. Albert Einstein 500, Cidade Universitária, Campinas, SP 13083-852 Brazil
| | - John A. Posada
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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Wang G, Haringa C, Tang W, Noorman H, Chu J, Zhuang Y, Zhang S. Coupled metabolic-hydrodynamic modeling enabling rational scale-up of industrial bioprocesses. Biotechnol Bioeng 2019; 117:844-867. [PMID: 31814101 DOI: 10.1002/bit.27243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/28/2019] [Accepted: 11/30/2019] [Indexed: 12/13/2022]
Abstract
Metabolomics aims to address what and how regulatory mechanisms are coordinated to achieve flux optimality, different metabolic objectives as well as appropriate adaptations to dynamic nutrient availability. Recent decades have witnessed that the integration of metabolomics and fluxomics within the goal of synthetic biology has arrived at generating the desired bioproducts with improved bioconversion efficiency. Absolute metabolite quantification by isotope dilution mass spectrometry represents a functional readout of cellular biochemistry and contributes to the establishment of metabolic (structured) models required in systems metabolic engineering. In industrial practices, population heterogeneity arising from fluctuating nutrient availability frequently leads to performance losses, that is reduced commercial metrics (titer, rate, and yield). Hence, the development of more stable producers and more predictable bioprocesses can benefit from a quantitative understanding of spatial and temporal cell-to-cell heterogeneity within industrial bioprocesses. Quantitative metabolomics analysis and metabolic modeling applied in computational fluid dynamics (CFD)-assisted scale-down simulators that mimic industrial heterogeneity such as fluctuations in nutrients, dissolved gases, and other stresses can procure informative clues for coping with issues during bioprocessing scale-up. In previous studies, only limited insights into the hydrodynamic conditions inside the industrial-scale bioreactor have been obtained, which makes case-by-case scale-up far from straightforward. Tracking the flow paths of cells circulating in large-scale bioreactors is a highly valuable tool for evaluating cellular performance in production tanks. The "lifelines" or "trajectories" of cells in industrial-scale bioreactors can be captured using Euler-Lagrange CFD simulation. This novel methodology can be further coupled with metabolic (structured) models to provide not only a statistical analysis of cell lifelines triggered by the environmental fluctuations but also a global assessment of the metabolic response to heterogeneity inside an industrial bioreactor. For the future, the industrial design should be dependent on the computational framework, and this integration work will allow bioprocess scale-up to the industrial scale with an end in mind.
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Affiliation(s)
- Guan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Cees Haringa
- Transport Phenomena, Chemical Engineering Department, Delft University of Technology, Delft, The Netherlands.,DSM Biotechnology Center, Delft, The Netherlands
| | - Wenjun Tang
- DSM Biotechnology Center, Delft, The Netherlands
| | - Henk Noorman
- DSM Biotechnology Center, Delft, The Netherlands.,Bioprocess Engineering, Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
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Li XR, Yang YK, Wang RB, An FL, Zhang YD, Nie JQ, Ahamada H, Liu XX, Liu CL, Deng Y, Bai ZH, Li Y, Liu XR. A scale-down model of 4000-L cell culture process for inactivated foot-and-mouth disease vaccine production. Vaccine 2019; 37:6380-6389. [PMID: 31519448 DOI: 10.1016/j.vaccine.2019.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/01/2019] [Accepted: 09/04/2019] [Indexed: 01/21/2023]
Abstract
The anticipated increasing demand for inactivated foot-and-mouth (FMD) disease vaccine calls for its larger production capacity, while development of a large-scale process typically requires high running cost and has very limited experimental throughput at manufacturing scale. Thus, an economic scale-down model of representing a large-scale process becomes necessary and essential. In this study, we used a systematic approach to establish a scale-down model representing a 4000-L culture process for FMD vaccine production by suspension BHK-21 cells. In detail, we firstly compared hydrodynamic properties of three bioreactors (14-L, 800-L and 4000-L) under three different conditions (equivalent mixing time, equivalent shear stress and equivalent volumetric power). We figured out equivalent volumetric power (P/V) potentially as an appropriate scale-down strategy, since it resulted in comparable calculated hydrodynamic parameters among three bioreactors. Next, we used computational fluid dynamics (CFD) simulation to provide more details about hydrodynamic environments inside the bioreactors, which supports the reliability of this scale-down strategy. Finally, we compared cell growth, metabolites, vaccine productivity and product quality attributes during FMD vaccine production by BHK-21 cells and observed very close performances among three bioreactors, which once again demonstrates the robustness of this scale-down model. This scale-down strategy can be applied to study variations and critical quality attributes (CQAs) in the resultant production process based on quality by design (QbD) principles, aiming at further more efficient optimization of vaccine production.
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Affiliation(s)
- Xin-Ran Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
| | - Yan-Kun Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Rong-Bin Wang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Fang-Lan An
- China Agricultural Veterinary Biological Science and Technology Co., Ltd, Lanzhou 730046, China
| | - Yun-De Zhang
- China Agricultural Veterinary Biological Science and Technology Co., Ltd, Lanzhou 730046, China
| | - Jian-Qi Nie
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
| | - Hadji Ahamada
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Xiu-Xia Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Chun-Li Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Zhong-Hu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China.
| | - Ye Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China.
| | - Xue-Rong Liu
- China Agricultural Veterinary Biological Science and Technology Co., Ltd, Lanzhou 730046, China.
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Reproduction of Large-Scale Bioreactor Conditions on Microfluidic Chips. Microorganisms 2019; 7:microorganisms7040105. [PMID: 31010155 PMCID: PMC6518007 DOI: 10.3390/microorganisms7040105] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/03/2019] [Accepted: 04/15/2019] [Indexed: 11/17/2022] Open
Abstract
Microbial cells in industrial large-scale bioreactors are exposed to fluctuating conditions, e.g., nutrient concentration, dissolved oxygen, temperature, and pH. These inhomogeneities can influence the cell physiology and metabolism, e.g., decelerate cell growth and product formation. Microfluidic systems offer new opportunities to study such effects in great detail by examining responses to varying environmental conditions at single-cell level. However, the possibility to reproduce large-scale bioreactor conditions in microscale cultivation systems has not yet been systematically investigated. Hence, we apply computational fluid dynamics (CFD) simulations to analyze and compare three commonly used microfluidic single-cell trapping and cultivation devices that are based on (i) mother machines (MM), (ii) monolayer growth chambers (MGC), and (iii) negative dielectrophoresis (nDEP). Several representative time-variant nutrient concentration profiles are applied at the chip entry. Responses to these input signals within the studied microfluidic devices are comparatively evaluated at the positions of the cultivated cells. The results are comprehensively presented in a Bode diagram that illustrates the degree of signal damping depending on the frequency of change in the inlet concentration. As a key finding, the MM can accurately reproduce signal changes that occur within 1 s or slower, which are typical for the environmental conditions observed by single cells in large-scale bioreactors, while faster changes are levelled out. In contrast, the nDEP and MGC are found to level out signal changes occurring within 10 s or faster, which can be critical for the proposed application.
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Tajsoleiman T, Mears L, Krühne U, Gernaey KV, Cornelissen S. An Industrial Perspective on Scale-Down Challenges Using Miniaturized Bioreactors. Trends Biotechnol 2019; 37:697-706. [PMID: 30737008 DOI: 10.1016/j.tibtech.2019.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 12/25/2022]
Abstract
Miniaturized stirred bioreactors (MSBRs) are gaining popularity as a cost-effective approach to scale-down experimentation. However, realizing conditions that reflect the large-scale process accurately can be challenging. This article highlights common challenges of using MSBRs for scale-down. The fundamental difference between oxygen mass transfer coefficient (kLa) and oxygen transfer rate scaling is addressed and the difficulty of achieving turbulent flow and industrially relevant tip speeds is described. More practical challenges of using MSBR systems for scale-down are also discussed, including the risk of vortex formation, changed volume dynamics, and wall growth. By highlighting these challenges, the article aims to create more awareness of these difficulties and to contribute to improved design of scale-down experiments.
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Affiliation(s)
- Tannaz Tajsoleiman
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark
| | - Lisa Mears
- Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
| | - Ulrich Krühne
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark
| | - Krist V Gernaey
- Process and Systems Engineering Center (PROSYS), Department of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kgs. Lyngby, Denmark. https://twitter.com/@KristGernaey
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Haringa C, Mudde RF, Noorman HJ. From industrial fermentor to CFD-guided downscaling: what have we learned? Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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40
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Zieringer J, Takors R. In Silico Prediction of Large-Scale Microbial Production Performance: Constraints for Getting Proper Data-Driven Models. Comput Struct Biotechnol J 2018; 16:246-256. [PMID: 30105090 PMCID: PMC6077756 DOI: 10.1016/j.csbj.2018.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/11/2018] [Accepted: 06/12/2018] [Indexed: 12/20/2022] Open
Abstract
Industrial bioreactors range from 10.000 to 700.000 L and characteristically show different zones of substrate availabilities, dissolved gas concentrations and pH values reflecting physical, technical and economic constraints of scale-up. Microbial producers are fluctuating inside the bioreactors thereby experiencing frequently changing micro-environmental conditions. The external stimuli induce responses on microbial metabolism and on transcriptional regulation programs. Both may deteriorate the expected microbial production performance in large scale compared to expectations deduced from ideal, well-mixed lab-scale conditions. Accordingly, predictive tools are needed to quantify large-scale impacts considering bioreactor heterogeneities. The review shows that the time is right to combine simulations of microbial kinetics with calculations of large-scale environmental conditions to predict the bioreactor performance. Accordingly, basic experimental procedures and computational tools are presented to derive proper microbial models and hydrodynamic conditions, and to link both for bioreactor modeling. Particular emphasis is laid on the identification of gene regulatory networks as the implementation of such models will surely gain momentum in future studies.
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41
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Heins AL, Weuster-Botz D. Population heterogeneity in microbial bioprocesses: origin, analysis, mechanisms, and future perspectives. Bioprocess Biosyst Eng 2018. [PMID: 29541890 DOI: 10.1007/s00449-018-1922-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Population heterogeneity is omnipresent in all bioprocesses even in homogenous environments. Its origin, however, is only so well understood that potential strategies like bet-hedging, noise in gene expression and division of labour that lead to population heterogeneity can be derived from experimental studies simulating the dynamics in industrial scale bioprocesses. This review aims at summarizing the current state of the different parts of single cell studies in bioprocesses. This includes setups to visualize different phenotypes of single cells, computational approaches connecting single cell physiology with environmental influence and special cultivation setups like scale-down reactors that have been proven to be useful to simulate large-scale conditions. A step in between investigation of populations and single cells is studying subpopulations with distinct properties that differ from the rest of the population with sub-omics methods which are also presented here. Moreover, the current knowledge about population heterogeneity in bioprocesses is summarized for relevant industrial production hosts and mixed cultures, as they provide the unique opportunity to distribute metabolic burden and optimize production processes in a way that is impossible in traditional monocultures. In the end, approaches to explain the underlying mechanism of population heterogeneity and the evidences found to support each hypothesis are presented. For instance, population heterogeneity serving as a bet-hedging strategy that is used as coordinated action against bioprocess-related stresses while at the same time spreading the risk between individual cells as it ensures the survival of least a part of the population in any environment the cells encounter.
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Affiliation(s)
- Anna-Lena Heins
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany.
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
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42
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Wang G, Zhao J, Haringa C, Tang W, Xia J, Chu J, Zhuang Y, Zhang S, Deshmukh AT, van Gulik W, Heijnen JJ, Noorman HJ. Comparative performance of different scale-down simulators of substrate gradients in Penicillium chrysogenum cultures: the need of a biological systems response analysis. Microb Biotechnol 2018; 11:486-497. [PMID: 29333753 PMCID: PMC5902331 DOI: 10.1111/1751-7915.13046] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/18/2017] [Accepted: 12/18/2017] [Indexed: 12/22/2022] Open
Abstract
In a 54 m3 large‐scale penicillin fermentor, the cells experience substrate gradient cycles at the timescales of global mixing time about 20–40 s. Here, we used an intermittent feeding regime (IFR) and a two‐compartment reactor (TCR) to mimic these substrate gradients at laboratory‐scale continuous cultures. The IFR was applied to simulate substrate dynamics experienced by the cells at full scale at timescales of tens of seconds to minutes (30 s, 3 min and 6 min), while the TCR was designed to simulate substrate gradients at an applied mean residence time (τc) of 6 min. A biological systems analysis of the response of an industrial high‐yielding P. chrysogenum strain has been performed in these continuous cultures. Compared to an undisturbed continuous feeding regime in a single reactor, the penicillin productivity (qPenG) was reduced in all scale‐down simulators. The dynamic metabolomics data indicated that in the IFRs, the cells accumulated high levels of the central metabolites during the feast phase to actively cope with external substrate deprivation during the famine phase. In contrast, in the TCR system, the storage pool (e.g. mannitol and arabitol) constituted a large contribution of carbon supply in the non‐feed compartment. Further, transcript analysis revealed that all scale‐down simulators gave different expression levels of the glucose/hexose transporter genes and the penicillin gene clusters. The results showed that qPenG did not correlate well with exposure to the substrate regimes (excess, limitation and starvation), but there was a clear inverse relation between qPenG and the intracellular glucose level.
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Affiliation(s)
- Guan Wang
- State key laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, China
| | - Junfei Zhao
- State key laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, China
| | - Cees Haringa
- Transport Phenomena, Chemical Engineering Department, Delft University of Technology, Delft, The Netherlands
| | - Wenjun Tang
- State key laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, China
| | - Jianye Xia
- State key laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, China
| | - Ju Chu
- State key laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, China
| | - Yingping Zhuang
- State key laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, China
| | - Siliang Zhang
- State key laboratory of Bioreactor Engineering, East China University of Science and Technology (ECUST), Shanghai, China
| | | | - Walter van Gulik
- Cell Systems Engineering, Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Joseph J Heijnen
- Cell Systems Engineering, Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Henk J Noorman
- DSM Biotechnology Center, Delft, The Netherlands.,Bio Process Engineering, Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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43
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Computational fluid dynamics simulation of an industrial P. chrysogenum fermentation with a coupled 9-pool metabolic model: Towards rational scale-down and design optimization. Chem Eng Sci 2018. [DOI: 10.1016/j.ces.2017.09.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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44
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Wang G, Wu B, Zhao J, Haringa C, Xia J, Chu J, Zhuang Y, Zhang S, Heijnen JJ, van Gulik W, Deshmukh AT, Noorman HJ. Power input effects on degeneration in prolonged penicillin chemostat cultures: A systems analysis at flux, residual glucose, metabolite, and transcript levels. Biotechnol Bioeng 2017; 115:114-125. [DOI: 10.1002/bit.26447] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/14/2017] [Accepted: 09/01/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Guan Wang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Baofeng Wu
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Junfei Zhao
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Cees Haringa
- Transport Phenomena, Chemical Engineering Department; Delft University of Technology; Delft The Netherlands
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology (ECUST); Shanghai People's Republic of China
| | - Joseph J. Heijnen
- Cell Systems Engineering, Department of Biotechnology; Delft University of Technology; Delft The Netherlands
| | - Walter van Gulik
- Cell Systems Engineering, Department of Biotechnology; Delft University of Technology; Delft The Netherlands
| | | | - Henk J. Noorman
- DSM Biotechnology Center; Delft The Netherlands
- Bio Process Engineering, Department of Biotechnology; Delft University of Technology; Delft The Netherlands
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45
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46
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Limberg MH, Joachim M, Klein B, Wiechert W, Oldiges M. pH fluctuations imperil the robustness of C. glutamicum to short term oxygen limitation. J Biotechnol 2017; 259:248-260. [DOI: 10.1016/j.jbiotec.2017.08.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 11/16/2022]
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47
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Haringa C, Deshmukh AT, Mudde RF, Noorman HJ. Euler-Lagrange analysis towards representative down-scaling of a 22 m 3 aerobic S. cerevisiae fermentation. Chem Eng Sci 2017. [DOI: 10.1016/j.ces.2017.01.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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48
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Jansen MLA, Bracher JM, Papapetridis I, Verhoeven MD, de Bruijn H, de Waal PP, van Maris AJA, Klaassen P, Pronk JT. Saccharomyces cerevisiae strains for second-generation ethanol production: from academic exploration to industrial implementation. FEMS Yeast Res 2017; 17:3868933. [PMID: 28899031 PMCID: PMC5812533 DOI: 10.1093/femsyr/fox044] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/15/2017] [Indexed: 11/18/2022] Open
Abstract
The recent start-up of several full-scale 'second generation' ethanol plants marks a major milestone in the development of Saccharomyces cerevisiae strains for fermentation of lignocellulosic hydrolysates of agricultural residues and energy crops. After a discussion of the challenges that these novel industrial contexts impose on yeast strains, this minireview describes key metabolic engineering strategies that have been developed to address these challenges. Additionally, it outlines how proof-of-concept studies, often developed in academic settings, can be used for the development of robust strain platforms that meet the requirements for industrial application. Fermentation performance of current engineered industrial S. cerevisiae strains is no longer a bottleneck in efforts to achieve the projected outputs of the first large-scale second-generation ethanol plants. Academic and industrial yeast research will continue to strengthen the economic value position of second-generation ethanol production by further improving fermentation kinetics, product yield and cellular robustness under process conditions.
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Affiliation(s)
- Mickel L. A. Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Jasmine M. Bracher
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Ioannis Papapetridis
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Maarten D. Verhoeven
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Hans de Bruijn
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Paul P. de Waal
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Antonius J. A. van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Paul Klaassen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
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49
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Binder D, Drepper T, Jaeger KE, Delvigne F, Wiechert W, Kohlheyer D, Grünberger A. Homogenizing bacterial cell factories: Analysis and engineering of phenotypic heterogeneity. Metab Eng 2017. [DOI: 10.1016/j.ymben.2017.06.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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50
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Tang W, Deshmukh AT, Haringa C, Wang G, van Gulik W, van Winden W, Reuss M, Heijnen JJ, Xia J, Chu J, Noorman HJ. A 9-pool metabolic structured kinetic model describing days to seconds dynamics of growth and product formation byPenicillium chrysogenum. Biotechnol Bioeng 2017; 114:1733-1743. [DOI: 10.1002/bit.26294] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/26/2017] [Accepted: 03/14/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Wenjun Tang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; P.O. Box 329#, No.130, Meilong Road Shanghai P.R. China
| | | | - Cees Haringa
- Cell Systems Engineering; Department of Biotechnology; Delft University of Technology; Delft The Netherlands
| | - Guan Wang
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; P.O. Box 329#, No.130, Meilong Road Shanghai P.R. China
| | - Walter van Gulik
- Cell Systems Engineering; Department of Biotechnology; Delft University of Technology; Delft The Netherlands
| | | | - Matthias Reuss
- Institute of Biochemical Engineering; University of Stuttgart; Stuttgart Germany
| | - Joseph J. Heijnen
- Cell Systems Engineering; Department of Biotechnology; Delft University of Technology; Delft The Netherlands
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; P.O. Box 329#, No.130, Meilong Road Shanghai P.R. China
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering; East China University of Science and Technology; P.O. Box 329#, No.130, Meilong Road Shanghai P.R. China
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