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Singh VK, Jiménez del Val I, Glassey J, Kavousi F. Integration Approaches to Model Bioreactor Hydrodynamics and Cellular Kinetics for Advancing Bioprocess Optimisation. Bioengineering (Basel) 2024; 11:546. [PMID: 38927782 PMCID: PMC11200465 DOI: 10.3390/bioengineering11060546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Large-scale bioprocesses are increasing globally to cater to the larger market demands for biological products. As fermenter volumes increase, the efficiency of mixing decreases, and environmental gradients become more pronounced compared to smaller scales. Consequently, the cells experience gradients in process parameters, which in turn affects the efficiency and profitability of the process. Computational fluid dynamics (CFD) simulations are being widely embraced for their ability to simulate bioprocess performance, facilitate bioprocess upscaling, downsizing, and process optimisation. Recently, CFD approaches have been integrated with dynamic Cell reaction kinetic (CRK) modelling to generate valuable information about the cellular response to fluctuating hydrodynamic parameters inside large production processes. Such coupled approaches have the potential to facilitate informed decision-making in intelligent biomanufacturing, aligning with the principles of "Industry 4.0" concerning digitalisation and automation. In this review, we discuss the benefits of utilising integrated CFD-CRK models and the different approaches to integrating CFD-based bioreactor hydrodynamic models with cellular kinetic models. We also highlight the suitability of different coupling approaches for bioprocess modelling in the purview of associated computational loads.
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Affiliation(s)
- Vishal Kumar Singh
- Process and Chemical Engineering, School of Engineering and Architecture, University College Cork, T12 K8AF Cork, Ireland;
| | - Ioscani Jiménez del Val
- School of Chemical & Bioprocess Engineering, University College Dublin, D04 V1W8 Dublin, Ireland;
| | - Jarka Glassey
- Process and Chemical Engineering, School of Engineering and Architecture, University College Cork, T12 K8AF Cork, Ireland;
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Fatemeh Kavousi
- Process and Chemical Engineering, School of Engineering and Architecture, University College Cork, T12 K8AF Cork, Ireland;
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2
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Gorter de Vries PJ, Mol V, Sonnenschein N, Jensen TØ, Nielsen AT. Probing efficient microbial CO 2 utilisation through metabolic and process modelling. Microb Biotechnol 2024; 17:e14414. [PMID: 38380934 PMCID: PMC10880515 DOI: 10.1111/1751-7915.14414] [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: 07/24/2023] [Revised: 11/29/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024] Open
Abstract
Acetogenic gas fermentation is increasingly studied as a promising technology to upcycle carbon-rich waste gasses. Currently the product range is limited, and production yields, rates and titres for a number of interesting products do not allow for economically viable processes. By pairing process modelling and host-agnostic metabolic modelling, we compare fermentation conditions and various products to optimise the processes. The models were then used in a simulation of an industrial-scale bubble column reactor. We find that increased temperatures favour gas transfer rates, particularly for the valuable and limiting H2 , while furthermore predicting an optimal feed composition of 9:1 mol H2 to mol CO2 . Metabolically, the increased non-growth associated maintenance requirements of thermophiles favours the formation of catabolic products. To assess the expansion of the product portfolio beyond acetate, both a product volatility analysis and a metabolic pathway model were implemented. In-situ recovery of volatile products is shown to be within range for acetone but challenging due to the extensive evaporation of water, while the direct production of more valuable compounds by acetogens is metabolically unfavourable compared to acetate and ethanol. We discuss alternative approaches to overcome these challenges to utilise acetogenic CO2 fixation to produce a wider range of carbon negative chemicals.
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Affiliation(s)
- Philip J. Gorter de Vries
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Viviënne Mol
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Nikolaus Sonnenschein
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKongens LyngbyDenmark
| | - Torbjørn Ølshøj Jensen
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
- AgainSøborgDenmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
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3
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Saur KM, Kiefel R, Niehoff PJ, Hofstede J, Ernst P, Brockkötter J, Gätgens J, Viell J, Noack S, Wierckx N, Büchs J, Jupke A. Holistic Approach to Process Design and Scale-Up for Itaconic Acid Production from Crude Substrates. Bioengineering (Basel) 2023; 10:723. [PMID: 37370654 DOI: 10.3390/bioengineering10060723] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Bio-based bulk chemicals such as carboxylic acids continue to struggle to compete with their fossil counterparts on an economic basis. One possibility to improve the economic feasibility is the use of crude substrates in biorefineries. However, impurities in these substrates pose challenges in fermentation and purification, requiring interdisciplinary research. This work demonstrates a holistic approach to biorefinery process development, using itaconic acid production on thick juice based on sugar beets with Ustilago sp. as an example. A conceptual process design with data from artificially prepared solutions and literature data from fermentation on glucose guides the simultaneous development of the upstream and downstream processes up to a 100 L scale. Techno-economic analysis reveals substrate consumption as the main constituent of production costs and therefore, the product yield is the driver of process economics. Aligning pH-adjusting agents in the fermentation and the downstream process is a central lever for product recovery. Experiments show that fermentation can be transferred from glucose to thick juice by changing the feeding profile. In downstream processing, an additional decolorization step is necessary to remove impurities accompanying the crude substrate. Moreover, we observe an increased use of pH-adjusting agents compared to process simulations.
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Affiliation(s)
- Katharina Maria Saur
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Robert Kiefel
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Paul-Joachim Niehoff
- Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Jordy Hofstede
- Process Systems Engineering (AVT.SVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Philipp Ernst
- Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1, 52428 Jülich, Germany
| | - Johannes Brockkötter
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Jochem Gätgens
- Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1, 52428 Jülich, Germany
| | - Jörn Viell
- Process Systems Engineering (AVT.SVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Stephan Noack
- Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1, 52428 Jülich, Germany
| | - Nick Wierckx
- Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1, 52428 Jülich, Germany
| | - Jochen Büchs
- Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Andreas Jupke
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, 52074 Aachen, Germany
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4
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Driessen JL, Johnsen J, Pogrebnyakov I, Mohamed ET, Mussatto SI, Feist AM, Jensen SI, Nielsen AT. Adaptive laboratory evolution of Bacillus subtilis to overcome toxicity of lignocellulosic hydrolysate derived from Distiller's dried grains with solubles (DDGS). Metab Eng Commun 2023; 16:e00223. [PMID: 37234932 PMCID: PMC10206485 DOI: 10.1016/j.mec.2023.e00223] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/03/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Microbial tolerance to toxic compounds formed during biomass pretreatment is a significant challenge to produce bio-based products from lignocellulose cost effectively. Rational engineering can be problematic due to insufficient prerequisite knowledge of tolerance mechanisms. Therefore, adaptive laboratory evolution was applied to obtain 20 tolerant lineages of Bacillus subtilis strains able to utilize Distiller's Dried Grains with Solubles-derived (DDGS) hydrolysate. Evolved strains showed both improved growth performance and retained heterologous enzyme production using 100% hydrolysate-based medium, whereas growth of the starting strains was essentially absent. Whole-genome resequencing revealed that evolved isolates acquired mutations in the global regulator codY in 15 of the 19 sequenced isolates. Furthermore, mutations in genes related to oxidative stress (katA, perR) and flagella function appeared in both tolerance and control evolution experiments without toxic compounds. Overall, tolerance adaptive laboratory evolution yielded strains able to utilize DDGS-hydrolysate to produce enzymes and hence proved to be a valuable tool for the valorization of lignocellulose.
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Affiliation(s)
- Jasper L.S.P. Driessen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Josefin Johnsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Ivan Pogrebnyakov
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Elsayed T.T. Mohamed
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Solange I. Mussatto
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800, Kongens Lyngby, Denmark
| | - Adam M. Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0412, USA
| | - Sheila I. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Alex T. Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
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Puiman L, Almeida Benalcázar E, Picioreanu C, Noorman HJ, Haringa C. Downscaling Industrial-Scale Syngas Fermentation to Simulate Frequent and Irregular Dissolved Gas Concentration Shocks. Bioengineering (Basel) 2023; 10:bioengineering10050518. [PMID: 37237589 DOI: 10.3390/bioengineering10050518] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
In large-scale syngas fermentation, strong gradients in dissolved gas (CO, H2) concentrations are very likely to occur due to locally varying mass transfer and convection rates. Using Euler-Lagrangian CFD simulations, we analyzed these gradients in an industrial-scale external-loop gas-lift reactor (EL-GLR) for a wide range of biomass concentrations, considering CO inhibition for both CO and H2 uptake. Lifeline analyses showed that micro-organisms are likely to experience frequent (5 to 30 s) oscillations in dissolved gas concentrations with one order of magnitude. From the lifeline analyses, we developed a conceptual scale-down simulator (stirred-tank reactor with varying stirrer speed) to replicate industrial-scale environmental fluctuations at bench scale. The configuration of the scale-down simulator can be adjusted to match a broad range of environmental fluctuations. Our results suggest a preference for industrial operation at high biomass concentrations, as this would strongly reduce inhibitory effects, provide operational flexibility and enhance the product yield. The peaks in dissolved gas concentration were hypothesized to increase the syngas-to-ethanol yield due to the fast uptake mechanisms in C. autoethanogenum. The proposed scale-down simulator can be used to validate such results and to obtain data for parametrizing lumped kinetic metabolic models that describe such short-term responses.
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Affiliation(s)
- Lars Puiman
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
| | - Eduardo Almeida Benalcázar
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
| | - Cristian Picioreanu
- Biological and Environmental Science and Engineering, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Henk J Noorman
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
- Royal DSM, Alexander Fleminglaan 1, 2613 Delft, The Netherlands
| | - Cees Haringa
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
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6
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Dynamic Interplay between O2 Availability, Growth Rates, and the Transcriptome of Yarrowia lipolytica. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Industrial-sized fermenters differ from the laboratory environment in which bioprocess development initially took place. One of the issues that can lead to reduced productivity on a large scale or even early termination of the process is the presence of bioreactor heterogeneities. This work proposes and adopts a design–build–test–learn-type workflow that estimates the substrate, oxygen, and resulting growth heterogeneities through a compartmental modelling approach and maps Yarrowia lipolytica-specific behavior in this relevant range of conditions. The results indicate that at a growth rate of 0.1 h−1, the largest simulated volume (90 m3) reached partial oxygen limitation. Throughout the fed-batch, the cells experienced dissolved oxygen values from 0 to 75% and grew at rates of 0 to 0.2 h−1. These simulated large-scale conditions were tested in small-scale cultivations, which elucidated a transcriptome with a strong downregulation of various transporter and central carbon metabolism genes during oxygen limitation. The relation between oxygen availability and differential gene expression was dynamic and did not show a simple on–off behavior. This indicates that Y. lipolytica can differentiate between different available oxygen concentrations and adjust its transcription accordingly. The workflow presented can be used for Y. lipolytica-based strain engineering, thereby accelerating bioprocess development.
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7
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Blöbaum L, Haringa C, Grünberger A. Microbial lifelines in bioprocesses: From concept to application. Biotechnol Adv 2023; 62:108071. [PMID: 36464144 DOI: 10.1016/j.biotechadv.2022.108071] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]
Abstract
Bioprocesses are scaled up for the production of large product quantities. With larger fermenter volumes, mixing becomes increasingly inefficient and environmental gradients get more prominent than in smaller scales. Environmental gradients have an impact on the microorganism's metabolism, which makes the prediction of large-scale performance difficult and can lead to scale-up failure. A promising approach for improved understanding and estimation of dynamics of microbial populations in large-scale bioprocesses is the analysis of microbial lifelines. The lifeline of a microbe in a bioprocess is the experience of environmental gradients from a cell's perspective, which can be described as a time series of position, environment and intracellular condition. Currently, lifelines are predominantly determined using models with computational fluid dynamics, but new technical developments in flow-following sensor particles and microfluidic single-cell cultivation open the door to a more interdisciplinary concept. We critically review the current concepts and challenges in lifeline determination and application of lifeline analysis, as well as strategies for the integration of these techniques into bioprocess development. Lifelines can contribute to a successful scale-up by guiding scale-down experiments and identifying strain engineering targets or bioreactor optimisations.
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Affiliation(s)
- Luisa Blöbaum
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Bielefeld, Germany; CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Cees Haringa
- Bioprocess Engineering, Applied Sciences/Biotechnology, TU, Delft, Netherlands
| | - Alexander Grünberger
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, Bielefeld, Germany; 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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8
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Gu W, Kavanagh JM, McClure DD. A scalable model for EPA and fatty acid production by Phaeodactylum tricornutum. Front Bioeng Biotechnol 2022; 10:1011570. [PMID: 36312541 PMCID: PMC9597327 DOI: 10.3389/fbioe.2022.1011570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/01/2022] [Indexed: 11/29/2022] Open
Abstract
Large-scale photoautotrophic production of microalgae has the potential to provide a sustainable supply of omega-3 fatty acids (eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)) for human and animal nutrition. This study presents a kinetic model for the EPA-producing microalga Phaeodactylum tricornutum in photoautotrophic conditions, with light and nitrogen being the growth limiting factors. The model was developed using a dataset obtained from bench-scale (5 L) cultures and was successfully validated against pilot-scale (50 L) cultures. This model is the first to predict the biomass and total fatty acid accumulation along with the EPA concentrations in the biomass and total fatty acid fraction for microalgae. The model was used to develop an optimized repeated-batch strategy; implementation of this led to increases in the biomass and EPA productivities of 50 and 20% respectively. This clearly indicates the potential of the model to be used as a tool in the design, optimization and scale-up of microalgal systems for EPA production.
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Affiliation(s)
- Wenjia Gu
- School of Chemical and Biomolecular Engineering, The University of Sydney, Darlington, NSW, Australia
| | - John M. Kavanagh
- School of Chemical and Biomolecular Engineering, The University of Sydney, Darlington, NSW, Australia
| | - Dale D. McClure
- Department of Chemical Engineering, College of Engineering, Design and Physical Sciences, Brunel University, London, United Kingdom
- *Correspondence: Dale D. McClure,
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9
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Varghese S, Dhanraj ND, Rebello S, Sindhu R, Binod P, Pandey A, Jisha MS, Awasthi MK. Leads and hurdles to sustainable microbial bioplastic production. CHEMOSPHERE 2022; 305:135390. [PMID: 35728665 DOI: 10.1016/j.chemosphere.2022.135390] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/11/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Indiscriminate usage, disposal and recalcitrance of petroleum-based plastics have led to its accumulation leaving a negative impact on the environment. Bioplastics, particularly microbial bioplastics serve as an ecologically sustainable solution to nullify the negative impacts of plastics. Microbial production of biopolymers like Polyhydroxyalkanoates, Polyhydroxybutyrates and Polylactic acid using renewable feedstocks as well as industrial wastes have gained momentum in the recent years. The current study outlays types of bioplastics, their microbial sources and applications in various fields. Scientific evidence on bioplastics has suggested a unique range of applications such as industrial, agricultural and medical applications. Though diverse microorganisms such as Alcaligenes latus, Burkholderia sacchari, Micrococcus species, Lactobacillus pentosus, Bacillus sp., Pseudomonas sp., Klebsiella sp., Rhizobium sp., Enterobacter sp., Escherichia sp., Azototobacter sp., Protomonas sp., Cupriavidus sp., Halomonas sp., Saccharomyces sp., Kluyveromyces sp., and Ralstonia sp. are known to produce bioplastics, the industrial production of bioplastics is still challenging. Thus this paper also provides deep insights on the advancements made to maximise production of bioplastics using different approaches such as metabolic engineering, rDNA technologies and multitude of cultivation strategies. Finally, the constraints to microbial bioplastic production and the future directions of research are briefed. Hence the present review emphasizes on the importance of using bioplastics as a sustainable alternative to petroleum based plastic products to diminish environmental pollution.
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Affiliation(s)
- Sherin Varghese
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, 686560, India
| | - N D Dhanraj
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, 686560, India
| | - Sharrel Rebello
- School of Food Science & Technology, Mahatma Gandhi University, Kottayam, Kerala, 686560, India
| | - Raveendran Sindhu
- Department of Food Technology, T K M Institute of Technology, Kollam, 691505, Kerala, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum, 695 019, Kerala, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR- Indian Institute for Toxicology Research (CSIR-IITR), 31 MG Marg, Lucknow, 226 001, India; Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, 248 007, Uttarakhand, India; Centre for Energy and Environmental Sustainability, Lucknow, 226 029, Uttar Pradesh, India
| | - M S Jisha
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, 686560, India.
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712 100, China.
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10
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Maluta F, Paglianti A, Montante G. Toward a robust CFD modelling approach for reliable hydrodynamics and mass transfer predictions in aerobic stirred fermenters. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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11
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Jadhav DA, Park SG, Pandit S, Yang E, Ali Abdelkareem M, Jang JK, Chae KJ. Scalability of microbial electrochemical technologies: Applications and challenges. BIORESOURCE TECHNOLOGY 2022; 345:126498. [PMID: 34890815 DOI: 10.1016/j.biortech.2021.126498] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 06/13/2023]
Abstract
During wastewater treatment, microbial electrochemical technologies (METs) are a promising means for in situ energy harvesting and resource recovery. The primary constraint for such systems is scaling them up from the laboratory to practical applications. Currently, most research (∼90%) has been limited to benchtop models because of bioelectrochemical, economic, and engineering design limitations. Field trials, i.e., 1.5 m3 bioelectric toilet, 1000 L microbial electrolysis cell and industrial applications of METs have been conducted, and their results serve as positive indicators of their readiness for practical applications. Multiple startup companies have invested in the pilot-scale demonstrations of METs for industrial effluent treatment. Recently, advances in membrane/electrode modification, understanding of microbe-electrode interaction, and feasibility of electrochemical redox reactions have provided new directions for realizing the practical application. This study reviews the scaling-up challenges, success stories for onsite use, and readiness level of METs for commercialization that is inexpensive and sustainable.
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Affiliation(s)
- Dipak A Jadhav
- Division of Civil, Environmental Engineering and Logistics System (Environmental Major), College of Ocean Science and Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea; Department of Agricultural Engineering, Maharashtra Institute of Technology, Aurangabad, Maharashtra 431010, India
| | - Sung-Gwan Park
- Division of Civil, Environmental Engineering and Logistics System (Environmental Major), College of Ocean Science and Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea
| | - Soumya Pandit
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida 201306, India
| | - Euntae Yang
- Department of Marine Environmental Engineering, Gyeongsang National University, Gyeongsangnam-do 53064, Republic of Korea
| | - Mohammad Ali Abdelkareem
- Department of Sustainable and Renewable Energy Engineering, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates; Center for Advanced Materials Research, University of Sharjah, 27272 Sharjah, United Arab Emirates; Chemical Engineering Department, Faculty of Engineering, Minia University, AlMinya, Egypt
| | - Jae-Kyung Jang
- National Institute of Agricultural Sciences, Department of Agricultural Engineering Energy and Environmental Engineering Division, 310 Nongsaengmyeong-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do, Republic of Korea
| | - Kyu-Jung Chae
- Division of Civil, Environmental Engineering and Logistics System (Environmental Major), College of Ocean Science and Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea.
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12
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Multi-Objective Sustainability Optimization of Biomass Residues to Ethanol via Gasification and Syngas Fermentation: Trade-Offs between Profitability, Energy Efficiency, and Carbon Emissions. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This work presents a strategy for optimizing the production process of ethanol via integrated gasification and syngas fermentation, a conversion platform of growing interest for its contribution to carbon recycling. The objective functions (minimum ethanol selling price (MESP), energy efficiency, and carbon footprint) were evaluated for the combinations of different input variables in models of biomass gasification, energy production from syngas, fermentation, and ethanol distillation, and a multi-objective genetic algorithm was employed for the optimization of the integrated process. Two types of waste feedstocks were considered, wood residues and sugarcane bagasse, with the former leading to lower MESP and a carbon footprint of 0.93 USD/L and 3 g CO2eq/MJ compared to 1.00 USD/L and 10 g CO2eq/MJ for sugarcane bagasse. The energy efficiency was found to be 32% in both cases. An uncertainty analysis was conducted to determine critical decision variables, which were found to be the gasification zone temperature, the split fraction of the unreformed syngas sent to the combustion chamber, the dilution rate, and the gas residence time in the bioreactor. Apart from the abovementioned objectives, other aspects such as water footprint, ethanol yield, and energy self-sufficiency were also discussed.
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13
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Blombach B, Grünberger A, Centler F, Wierckx N, Schmid J. Exploiting unconventional prokaryotic hosts for industrial biotechnology. Trends Biotechnol 2021; 40:385-397. [PMID: 34482995 DOI: 10.1016/j.tibtech.2021.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022]
Abstract
Developing cost-efficient biotechnological processes is a major challenge in replacing fossil-based industrial production processes. The remarkable progress in genetic engineering ensures efficient and fast tailoring of microbial metabolism for a wide range of bioconversions. However, improving intrinsic properties such as tolerance, handling, growth, and substrate consumption rates is still challenging. At the same time, synthetic biology tools are becoming easier applicable and transferable to nonmodel organisms. These trends have resulted in the exploitation of new and unconventional microbial systems with sophisticated properties, which render them promising hosts for the bio-based industry. Here, we highlight the metabolic and cellular capabilities of representative prokaryotic newcomers and discuss the potential and drawbacks of these hosts for industrial application.
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Affiliation(s)
- Bastian Blombach
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany; SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
| | | | - Florian Centler
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Nick Wierckx
- Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1: Biotechnology, Jülich, Germany
| | - Jochen Schmid
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany.
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15
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Zhuang S, Renault N, Archer I. A brief review on recent development of multidisciplinary engineering in fermentation of Saccharomyces cerevisiae. J Biotechnol 2021; 339:32-41. [PMID: 34339775 DOI: 10.1016/j.jbiotec.2021.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 07/13/2021] [Accepted: 07/27/2021] [Indexed: 11/26/2022]
Abstract
Fermentation technology has unprecedented potential to upgrade state-of-art biotechnology and refine the processes used in existing ones, taking into account of complex technical, economic and environmental factors. Given the economic importance and ongoing challenges of biotech sector, multidisciplinary engineering technologies is poised to become an increasingly important tool along with the emergence of modern technology and innovation. This article reviews recent technology advancement in the field of fermentation using Saccharomyces cerevisiae. Interesting research progress has been made by leveraging multiple engineering fields such as electrical engineering, information engineering, electrochemical engineering and new material development, leading to recent development of novel real-time probes (electronic nose technology, analysis of yeast morphology and metabolites, timely control of glucose feed), improved understanding of electro-fermentation (enhanced electronic transfer provision), as well as application of cost-effective and sustainable materials (bioreactor vessel manufactured from textile, and yeast immobilisation support matrix made from abundant natural biomass). To the best of our knowledge, the subject is reviewed for the first time in recent years. Furthermore, this review also constitutes a futuristic S. cerevisiae fermentation process based on the recent advancement discussed.
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Affiliation(s)
- Shiwen Zhuang
- Industrial Biotechnology Innovation Centre (IBioIC), University of Strathclyde, Glasgow, G1 1XQ, United Kingdom; School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, United Kingdom.
| | - Neil Renault
- Industrial Biotechnology Innovation Centre (IBioIC), University of Strathclyde, Glasgow, G1 1XQ, United Kingdom; School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, United Kingdom
| | - Ian Archer
- Industrial Biotechnology Innovation Centre (IBioIC), University of Strathclyde, Glasgow, G1 1XQ, United Kingdom
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16
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Vollmer NI, Al R, Gernaey KV, Sin G. Synergistic optimization framework for the process synthesis and design of biorefineries. Front Chem Sci Eng 2021. [DOI: 10.1007/s11705-021-2071-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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17
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Two-fluids RANS predictions of gas cavities, power consumption, mixing time and oxygen transfer rate in an aerated fermenter scale-down stirred with multiple impellers. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107867] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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18
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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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19
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Khatami K, Perez-Zabaleta M, Owusu-Agyeman I, Cetecioglu Z. Waste to bioplastics: How close are we to sustainable polyhydroxyalkanoates production? WASTE MANAGEMENT (NEW YORK, N.Y.) 2021; 119:374-388. [PMID: 33139190 DOI: 10.1016/j.wasman.2020.10.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Increased awareness of environmental sustainability with associated strict environmental regulations has incentivized the pursuit of novel materials to replace conventional petroleum-derived plastics. Polyhydroxyalkanoates (PHAs) are appealing intracellular biopolymers and have drawn significant attention as a viable alternative to petrochemical based plastics not only due to their comparable physiochemical properties but also, their outstanding characteristics such as biodegradability and biocompatibility. This review provides a comprehensive overview of the recent developments on the involved PHA producer microorganisms, production process from different waste streams by both pure and mixed microbial cultures (MMCs). Bio-based PHA production, particularly using cheap carbon sources with MMCs, is getting more attention. The main bottlenecks are the low production yield and the inconsistency of the biopolymers. Bioaugmentation and metabolic engineering together with cost effective downstream processing are promising approaches to overcome the hurdles of commercial PHA production from waste streams.
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Affiliation(s)
- Kasra Khatami
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Mariel Perez-Zabaleta
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Isaac Owusu-Agyeman
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Zeynep Cetecioglu
- Department of Chemical Engineering, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden.
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20
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Gargalo CL, de Las Heras SC, Jones MN, Udugama I, Mansouri SS, Krühne U, Gernaey KV. Towards the Development of Digital Twins for the Bio-manufacturing Industry. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 176:1-34. [PMID: 33349908 DOI: 10.1007/10_2020_142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The bio-manufacturing industry, along with other process industries, now has the opportunity to be engaged in the latest industrial revolution, also known as Industry 4.0. To successfully accomplish this, a physical-to-digital-to-physical information loop should be carefully developed. One way to achieve this is, for example, through the implementation of digital twins (DTs), which are virtual copies of the processes. Therefore, in this paper, the focus is on understanding the needs and challenges faced by the bio-manufacturing industry when dealing with this digitalized paradigm. To do so, two major building blocks of a DT, data and models, are highlighted and discussed. Hence, firstly, data and their characteristics and collection strategies are examined as well as new methods and tools for data processing. Secondly, modelling approaches and their potential of being used in DTs are reviewed. Finally, we share our vision with regard to the use of DTs in the bio-manufacturing industry aiming at bringing the DT a step closer to its full potential and realization.
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Affiliation(s)
- Carina L Gargalo
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | | | - Mark Nicholas Jones
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark.,Molecular Quantum Solutions ApS, Copenhagen, Denmark
| | - Isuru Udugama
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Seyed Soheil Mansouri
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Ulrich Krühne
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Krist V Gernaey
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark.
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21
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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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22
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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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23
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Bioprocess intensification: Cases that (don't) work. N Biotechnol 2020; 61:108-115. [PMID: 33221394 DOI: 10.1016/j.nbt.2020.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 11/22/2022]
Abstract
Development of affordable and low carbon biobased manufacturing depends critically on strategies that reduce cost and emission profiles. This paper indicates that efforts around the reduction of capital costs by intensification of process equipment need to be carefully weighed against the inherently fast increasing financial and climate costs of driving forces used for the intensification. The fundamental relation between capital expenditures (CAPEX) and operational expenditures (OPEX) of intensified and non-intensified biobased processes and their financial and climatic impacts are emphasized and provisionally explored for a few industrial processes. General learnings flag the importance in particular of OPEX minimisation for sustainable bio-economic development.
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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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25
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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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26
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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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27
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Woodley JM. Advances in biological conversion technologies: new opportunities for reaction engineering. REACT CHEM ENG 2020. [DOI: 10.1039/c9re00422j] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reaction engineering needs to embrace biological conversion technologies, on the road to identify more sustainable routes for chemical manufacture.
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Affiliation(s)
- John M. Woodley
- Department of Chemical and Biochemical Engineering
- Technical University of Denmark (DTU)
- DK-2800 Kgs. Lyngby
- Denmark
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28
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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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29
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Grand Research Challenges for Sustainable Industrial Biotechnology. Trends Biotechnol 2019; 37:1042-1050. [DOI: 10.1016/j.tibtech.2019.04.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 01/23/2023]
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30
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Crater JS, Lievense JC. Scale-up of industrial microbial processes. FEMS Microbiol Lett 2019; 365:5026621. [PMID: 29860483 PMCID: PMC5995164 DOI: 10.1093/femsle/fny138] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/31/2018] [Indexed: 11/29/2022] Open
Abstract
Scaling up industrial microbial processes for commercial production is a high-stakes endeavor, requiring time and investment often exceeding that for laboratory microbe and process development. Omissions, oversights and errors can be costly, even fatal to the program. Approached properly, scale-up can be executed successfully. Three guiding principles are provided as a basis: begin with the end in mind; be diligent in the details; prepare for the unexpected. A detailed roadmap builds on these principles. There is a special emphasis on the fermentation step, which is usually the costliest and also impacts downstream processing. Examples of common scale-up mistakes and the recommended approaches are given. It is advised that engineering resources skilled in integrated process development and scale-up be engaged from the very beginning of microbe and process development to guide ongoing R&D, thus ensuring a smooth and profitable path to the large-scale commercial end.
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Affiliation(s)
- Jason S Crater
- Process Deployment, Genomatica Inc - Process Technology, San Diego, USA
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31
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Perez-Zabaleta M, Guevara-Martínez M, Gustavsson M, Quillaguamán J, Larsson G, van Maris AJA. Comparison of engineered Escherichia coli AF1000 and BL21 strains for (R)-3-hydroxybutyrate production in fed-batch cultivation. Appl Microbiol Biotechnol 2019; 103:5627-5639. [PMID: 31104101 PMCID: PMC6597613 DOI: 10.1007/s00253-019-09876-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/18/2019] [Accepted: 04/24/2019] [Indexed: 02/06/2023]
Abstract
Accumulation of acetate is a limiting factor in recombinant production of (R)-3-hydroxybutyrate (3HB) by Escherichia coli in high-cell-density processes. To alleviate this limitation, this study investigated two approaches: (i) deletion of phosphotransacetylase (pta), pyruvate oxidase (poxB), and/or the isocitrate lyase regulator (iclR), known to decrease acetate formation, on bioreactor cultivations designed to achieve high 3HB concentrations. (ii) Screening of different E. coli strain backgrounds (B, BL21, W, BW25113, MG1655, W3110, and AF1000) for their potential as low acetate-forming, 3HB-producing platforms. Deletion of pta and pta-poxB in the AF1000 strain background was to some extent successful in decreasing acetate formation, but also dramatically increased excretion of pyruvate and did not result in increased 3HB production in high-cell-density fed-batch cultivations. Screening of the different E. coli strains confirmed BL21 as a low acetate-forming background. Despite low 3HB titers in low-cell-density screening, 3HB-producing BL21 produced five times less acetic acid per mole of 3HB, which translated into a 2.3-fold increase in the final 3HB titer and a 3-fold higher volumetric 3HB productivity over 3HB-producing AF1000 strains in nitrogen-limited fed-batch cultivations. Consequently, the BL21 strain achieved the hitherto highest described volumetric productivity of 3HB (1.52 g L−1 h−1) and the highest 3HB concentration (16.3 g L−1) achieved by recombinant E. coli. Screening solely for 3HB titers in low-cell-density batch cultivations would not have identified the potential of this strain, reaffirming the importance of screening with the final production conditions in mind.
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Affiliation(s)
- Mariel Perez-Zabaleta
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
- Center of Biotechnology, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Mónica Guevara-Martínez
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
- Center of Biotechnology, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Martin Gustavsson
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
| | - Jorge Quillaguamán
- Center of Biotechnology, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Gen Larsson
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
| | - Antonius J. A. van Maris
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), Department of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-10691 Stockholm, Sweden
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32
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Baldanza VAR, Souza FG, Filho ST, Franco HA, Oliveira GE, Caetano RMJ, Hernandez JAR, Ferreira Leite SG, Furtado Sousa AM, Nazareth Silva AL. Controlled-release fertilizer based on poly(butylene succinate)/urea/clay and its effect on lettuce growth. J Appl Polym Sci 2018. [DOI: 10.1002/app.46858] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- V. A. R. Baldanza
- Instituto de Macromoléculas Professora Eloisa Mano; Universidade Federal do Rio de Janeiro, CT, Avenue Horácio Macedo, 2030, bloco J; Rio de Janeiro Brazil
| | - F. G. Souza
- Instituto de Macromoléculas Professora Eloisa Mano; Universidade Federal do Rio de Janeiro, CT, Avenue Horácio Macedo, 2030, bloco J; Rio de Janeiro Brazil
- Programa de Engenharia Civil; COPPE, Centro de Tecnologia - Cidade Universitária, Universidade Federal de Rio de Janeiro, Avenue Horácio Macedo, 2030, bloco I; Rio de Janeiro 21941-450 Brazil
| | - S. T. Filho
- Instituto Federal do Rio de Janeiro - IFRJ - Laboratório Multidisciplinar de Tecnologia Agroambiental - Campus Pinheiral; Pinheiral Rio de Janeiro Brazil
| | - H. A. Franco
- Instituto Federal do Rio de Janeiro - IFRJ - Laboratório Multidisciplinar de Tecnologia Agroambiental - Campus Pinheiral; Pinheiral Rio de Janeiro Brazil
| | - G. E. Oliveira
- Programa de Engenharia Civil; COPPE, Centro de Tecnologia - Cidade Universitária, Universidade Federal de Rio de Janeiro, Avenue Horácio Macedo, 2030, bloco I; Rio de Janeiro 21941-450 Brazil
| | - R. M. J. Caetano
- Programa de Engenharia Ambiental, Escola Politécnica, CT; Universidade Federal do Rio de Janeiro, Avenue Athos da Silveira Ramos, 149, Bloco A; Rio de Janeiro 21941-909 Brazil
| | - J. A. R. Hernandez
- Escola de Química; Universidade Federal do Rio de Janeiro, CT, Avenue Athos da Silveira Ramos, 149, Bloco E; Rio de Janeiro 21941-909 Brazil
| | - S. G. Ferreira Leite
- Escola de Química; Universidade Federal do Rio de Janeiro, CT, Avenue Athos da Silveira Ramos, 149, Bloco E; Rio de Janeiro 21941-909 Brazil
| | - A. M. Furtado Sousa
- Instituto de Química; Universidade do Estado do Rio de Janeiro, R. São Francisco Xavier, 524; Rio de Janeiro 20550-900 Brazil
| | - A. L. Nazareth Silva
- Instituto de Macromoléculas Professora Eloisa Mano; Universidade Federal do Rio de Janeiro, CT, Avenue Horácio Macedo, 2030, bloco J; Rio de Janeiro Brazil
- Programa de Engenharia Ambiental, Escola Politécnica, CT; Universidade Federal do Rio de Janeiro, Avenue Athos da Silveira Ramos, 149, Bloco A; Rio de Janeiro 21941-909 Brazil
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Hong EY, Kim JY, Upadhyay R, Park BJ, Lee JM, Kim BG. Rational engineering of ornithine decarboxylase with greater selectivity for ornithine over lysine through protein network analysis. J Biotechnol 2018; 281:175-182. [DOI: 10.1016/j.jbiotec.2018.07.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 07/03/2018] [Accepted: 07/14/2018] [Indexed: 01/09/2023]
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Hong EY, Lee SG, Park BJ, Lee JM, Yun H, Kim BG. Simultaneously Enhancing the Stability and Catalytic Activity of Multimeric Lysine Decarboxylase CadA by Engineering Interface Regions for Enzymatic Production of Cadaverine at High Concentration of Lysine. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700278] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/08/2017] [Indexed: 01/25/2023]
Affiliation(s)
- Eun Young Hong
- School of Chemical and Biological Engineering; Seoul National University; Seoul South Korea
| | - Sun-Gu Lee
- Department of Chemical Engineering; Pusan National University; Busan 609-735 South Korea
| | - Byung Jun Park
- School of Chemical and Biological Engineering; Seoul National University; Seoul South Korea
| | - Jong Min Lee
- School of Chemical and Biological Engineering; Seoul National University; Seoul South Korea
| | - Hyungdon Yun
- Department of Bioscience and Biotechnology; Konkuk University; Seoul South Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering; Seoul National University; Seoul South Korea
- Institute of Bioengineering; Seoul National University; Seoul South Korea
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Delvigne F, Takors R, Mudde R, van Gulik W, Noorman H. Bioprocess scale-up/down as integrative enabling technology: from fluid mechanics to systems biology and beyond. Microb Biotechnol 2017; 10:1267-1274. [PMID: 28805306 PMCID: PMC5609235 DOI: 10.1111/1751-7915.12803] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/12/2017] [Indexed: 11/28/2022] Open
Abstract
Efficient optimization of microbial processes is a critical issue for achieving a number of sustainable development goals, considering the impact of microbial biotechnology in agrofood, environment, biopharmaceutical and chemical industries. Many of these applications require scale-up after proof of concept. However, the behaviour of microbial systems remains unpredictable (at least partially) when shifting from laboratory-scale to industrial conditions. The need for robust microbial systems is thus highly needed in this context, as well as a better understanding of the interactions between fluid mechanics and cell physiology. For that purpose, a full scale-up/down computational framework is already available. This framework links computational fluid dynamics (CFD), metabolic flux analysis and agent-based modelling (ABM) for a better understanding of the cell lifelines in a heterogeneous environment. Ultimately, this framework can be used for the design of scale-down simulators and/or metabolically engineered cells able to cope with environmental fluctuations typically found in large-scale bioreactors. However, this framework still needs some refinements, such as a better integration of gas-liquid flows in CFD, and taking into account intrinsic biological noise in ABM.
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Affiliation(s)
- Frank Delvigne
- TERRA Research CenterMicrobial Processes and Interactions (MiPI)University of LiègeLiègeBelgium
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Rob Mudde
- Transport Phenomena SectionDepartment of Chemical EngineeringDelft University of TechnologyDelftThe Netherlands
| | - Walter van Gulik
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Henk Noorman
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
- DSM Biotechnology CenterDelftThe Netherlands
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Delvigne F, Noorman H. Scale-up/Scale-down of microbial bioprocesses: a modern light on an old issue. Microb Biotechnol 2017; 10:685-687. [PMID: 28556613 PMCID: PMC5481528 DOI: 10.1111/1751-7915.12732] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 12/22/2022] Open
Abstract
The bio‐economy is in transit from innovation to commercialization. The bioprocess industry is expected to increasingly deliver bio‐products to the market, in large amounts, at high quality and at competitive cost levels. This requires flawless start‐up of new large‐scale bioprocesses and continuous improvement of running processes. Fermentation scale‐up and operation can benefit from recent advances in three areas: 1. computation‐driven design of scale‐down simulators, 2. omics‐driven metabolic engineering and 3. sensing and understanding of population heterogeneity. Integration of these fields requires a unified computational approach, linked to big data and simulated reality frameworks, of which the contours are becoming visible today.
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Affiliation(s)
- Frank Delvigne
- TERRA Research Center, Microbial Processes and Interactions (MiPI), University of Liège, Liège, Belgium
| | - Henk Noorman
- DSM Biotechnology Center, Delft, The Netherlands.,Department of Biotechnology, Technical University Delft, Delft, The Netherlands
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