1
|
Rubio-Ribeaux D, da Costa RAM, Montero-Rodríguez D, do Amaral Marques NSA, Puerta-Díaz M, de Souza Mendonça R, Franco PM, Dos Santos JC, da Silva SS. Sustainable production of bioemulsifiers, a critical overview from microorganisms to promising applications. World J Microbiol Biotechnol 2023; 39:195. [PMID: 37171665 DOI: 10.1007/s11274-023-03611-6] [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: 02/16/2023] [Accepted: 04/06/2023] [Indexed: 05/13/2023]
Abstract
Microbial bioemulsifiers are molecules of amphiphilic nature and high molecular weight that are efficient in emulsifying two immiscible phases such as water and oil. These molecules are less effective in reducing surface tension and are synthesized by bacteria, yeast and filamentous fungi. Unlike synthetic emulsifiers, microbial bioemulsifiers have unique advantages such as biocompatibility, non-toxicity, biodegradability, efficiency at low concentrations and high selectivity under different conditions of pH, temperature and salinity. The adoption of microbial bioemulsifiers as alternatives to their synthetic counterparts has been growing in ongoing research. This article analyzes the production of microbial-based emulsifiers, the raw materials and fermentation processes used, as well as the scale-up and commercial applications of some of these biomolecules. The current trend of incorporating natural compounds into industrial formulations indicates that the search for new bioemulsifiers will continue to increase, with emphasis on performance improvement and economically viable processes.
Collapse
Affiliation(s)
- Daylin Rubio-Ribeaux
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, São Paulo, 12.602-810, Brazil.
- Faculty of Philosophy and Sciences, Campus Marília, São Paulo State University, São Paulo, 17.525-900, Brazil.
| | - Rogger Alessandro Mata da Costa
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, São Paulo, 12.602-810, Brazil
- Faculty of Philosophy and Sciences, Campus Marília, São Paulo State University, São Paulo, 17.525-900, Brazil
| | - Dayana Montero-Rodríguez
- Nucleus of Research in Environmental Sciences and Biotechnology, Catholic University of Pernambuco, Recife, Pernambuco, 50050-590, Brazil
- Faculty of Philosophy and Sciences, Campus Marília, São Paulo State University, São Paulo, 17.525-900, Brazil
| | - Nathália Sá Alencar do Amaral Marques
- Nucleus of Research in Environmental Sciences and Biotechnology, Catholic University of Pernambuco, Recife, Pernambuco, 50050-590, Brazil
- Faculty of Philosophy and Sciences, Campus Marília, São Paulo State University, São Paulo, 17.525-900, Brazil
| | - Mirelys Puerta-Díaz
- Pernambuco Institute of Agronomy, Recife, Pernambuco, 50761-000, Brazil
- Faculty of Philosophy and Sciences, Campus Marília, São Paulo State University, São Paulo, 17.525-900, Brazil
| | - Rafael de Souza Mendonça
- Nucleus of Research in Environmental Sciences and Biotechnology, Catholic University of Pernambuco, Recife, Pernambuco, 50050-590, Brazil
- Faculty of Philosophy and Sciences, Campus Marília, São Paulo State University, São Paulo, 17.525-900, Brazil
| | - Paulo Marcelino Franco
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, São Paulo, 12.602-810, Brazil
- Faculty of Philosophy and Sciences, Campus Marília, São Paulo State University, São Paulo, 17.525-900, Brazil
| | - Júlio César Dos Santos
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, São Paulo, 12.602-810, Brazil
- Faculty of Philosophy and Sciences, Campus Marília, São Paulo State University, São Paulo, 17.525-900, Brazil
| | - Silvio Silvério da Silva
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, São Paulo, 12.602-810, Brazil
- Faculty of Philosophy and Sciences, Campus Marília, São Paulo State University, São Paulo, 17.525-900, Brazil
| |
Collapse
|
2
|
Cao J, Chande C, Köhler JM. Microtoxicology by microfluidic instrumentation: a review. LAB ON A CHIP 2022; 22:2600-2623. [PMID: 35678285 DOI: 10.1039/d2lc00268j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Microtoxicology is concerned with the toxic effects of small amounts of substances. This review paper discusses the application of small amounts of noxious substances for toxicological investigation in small volumes. The vigorous development of miniaturized methods in microfluidics over the last two decades involves chip-based devices, micro droplet-based procedures, and the use of micro-segmented flow for microtoxicological studies. The studies have shown that the microfluidic approach is particularly valuable for highly parallelized and combinatorial dose-response screenings. Accurate dosing and mixing of effector substances in large numbers of microcompartments supplies detailed data of dose-response functions by highly concentration-resolved assays and allows evaluation of stochastic responses in case of small separated cell ensembles and single cell experiments. The investigations demonstrate that very different biological targets can be studied using miniaturized approaches, among them bacteria, eukaryotic microorganisms, cell cultures from tissues of multicellular organisms, stem cells, and early embryonic states. Cultivation and effector exposure tests can be performed in small volumes over weeks and months, confirming that the microfluicial strategy is also applicable for slow-growing organisms. Here, the state of the art of miniaturized toxicology, particularly for studying antibiotic susceptibility, drug toxicity testing in the miniaturized system like organ-on-chip, environmental toxicology, and the characterization of combinatorial effects by two and multi-dimensional screenings, is discussed. Additionally, this review points out the practical limitations of the microtoxicology platform and discusses perspectives on future opportunities and challenges.
Collapse
Affiliation(s)
- Jialan Cao
- Techn. Univ. Ilmenau, Dept. Phys. Chem. and Microreaction Technology, Institute for Micro- und Nanotechnologies/Institute for Chemistry and Biotechnology, Ilmenau, Germany.
| | - Charmi Chande
- Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - J Michael Köhler
- Techn. Univ. Ilmenau, Dept. Phys. Chem. and Microreaction Technology, Institute for Micro- und Nanotechnologies/Institute for Chemistry and Biotechnology, Ilmenau, Germany.
| |
Collapse
|
3
|
Fan Z, Tong N, Zhuang Z, Ma C, Ma J, Ju J, Duan Y, Zhu X. Medium optimization and subsequent fermentative regulation enabled the scaled-up production of anti-tuberculosis drug leads ilamycin-E1/E2. Biotechnol J 2022; 17:e2100427. [PMID: 35098690 DOI: 10.1002/biot.202100427] [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: 08/09/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/11/2022]
Abstract
BACKGROUND Tuberculosis (TB) and its evolving drug resistance have exerted severe threats on the global health, hence it is still essential to develop novel anti-TB antibiotics. Ilamycin-E1/E2 is a pair of cycloheptapeptide enantiomers obtained from a marine Streptomyces atratus SCSIO ZH16-ΔilaR mutant, and have presented significant anti-TB activities as promising drug lead compounds, but their clinical development has been hampered by low fermentation titers. MAIN METHODS AND MAJOR RESULTS By applying the statistical Plackett-Burman design (PBD) model, bacterial peptone was first screened out as the only significant but negative factor to affect the ilamycin-E1/E2 production. Subsequent single factor optimization in shaking flasks revealed that the replacement of bacterial peptone with malt extract could not only eliminate the accumulation of porphyrin-type competitive byproducts, but also improve the titer of ilamycin-E1/E2 from original 13.6±0.8 to 142.7±5.7 mg/L, about 10.5-fold increase. Next, a pH coordinated feeding strategy was adopted in 30L fermentor and obtained 169.8±2.5 mg/L ilamycin-E1/E2, but further scaled-up production in 300L fermentor only gave a titer of 131.5±7.5 mg/L due to the unsynchronization of feeding response and pH change. Consequently, a continuous pulse feeding strategy was utilized in 300L fermentor to solve the above problem and finally achieved 415.7±29.2 mg/L ilamycin-E1/E2, representing a 30.5-fold improvement. IMPLICATION Our work has provided a solid basis to acquire sufficient ilamycin-E1/E2 lead compounds and then support their potential anti-TB drug development. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Zhiying Fan
- Xiangya International Academy of Translational Medicine, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Nian Tong
- Xiangya International Academy of Translational Medicine, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Zhoukang Zhuang
- Xiangya International Academy of Translational Medicine, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Cheng Ma
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan, 410013, China
| | - Junying Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan, 410013, China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China.,Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discovery, Changsha, China.,National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan, 410013, China
| |
Collapse
|
4
|
Golombek F, Haumann M, Knoll MS, Fröba AP, Castiglione K. Three Steps, Two Enzymes, One Pot, but a Multitude of Nanocompartments: Combined Cycles of Kinetic Resolutions and Re-racemization with Incompatible Biocatalysts. ACS OMEGA 2021; 6:29192-29200. [PMID: 34746608 PMCID: PMC8567398 DOI: 10.1021/acsomega.1c04694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/04/2021] [Indexed: 06/01/2023]
Abstract
Deracemizations are clearly preferable to kinetic resolutions in the production of chiral molecules from racemates, as they allow up to 100% chemical and optical yield. Here we present a new process route for multienzymatic deracemizations that is relevant for reaction systems with incompatible reaction conditions of the biocatalysts. This often applies to combinations of lipases used for stereoselective acylation and solvent-sensitive racemases. By encapsulating a model racemase in polymeric vesicles, it was protected from inactivation by the organic solvent up to phase proportions of 99%. As high yields in the lipase reaction required either water proportions well below 1% or racemase-denaturating acyl donor concentrations, a one-pot reaction was implemented through the sequential use of lipase and racemase-containing nanocompartments. This strategy allowed us to perform two kinetic resolutions with intermittent re-racemization in one pot yielding 72% (0.72 mM after 120 h) of an enantiopure product.
Collapse
Affiliation(s)
- Florian Golombek
- Department
of Chemical and Biological Engineering, Institute of Bioprocess Engineering, Friedrich-Alexander University Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen, Germany
| | - Marco Haumann
- Department
Chemie- und Bioingenieurwesen, Lehrstuhl für Chemische Reaktionstechnik
(CRT), Friedrich-Alexander Universität
Erlangen-Nürnberg (FAU), Egerlandstr. 3, Erlangen 91058, Germany
| | - Matthias S.G. Knoll
- Department
of Chemical and Biological Engineering, Institute of Advanced Optical
Technologies − Thermophysical Properties, Friedrich-Alexander University Erlangen-Nürnberg, Paul-Gordan-Str. 8, Erlangen 91052, Germany
- Erlangen
Graduate School of Advanced Optical Technologies (SAOT), Friedrich-Alexander University Erlangen-Nürnberg,
Paul-Gordan-Str. 6, 91052 Erlangen, Germany
| | - Andreas Paul Fröba
- Department
of Chemical and Biological Engineering, Institute of Advanced Optical
Technologies − Thermophysical Properties, Friedrich-Alexander University Erlangen-Nürnberg, Paul-Gordan-Str. 8, Erlangen 91052, Germany
- Erlangen
Graduate School of Advanced Optical Technologies (SAOT), Friedrich-Alexander University Erlangen-Nürnberg,
Paul-Gordan-Str. 6, 91052 Erlangen, Germany
| | - Kathrin Castiglione
- Department
of Chemical and Biological Engineering, Institute of Bioprocess Engineering, Friedrich-Alexander University Erlangen-Nürnberg, Paul-Gordan-Str. 3, 91052 Erlangen, Germany
| |
Collapse
|
5
|
Contact-free infrared OD measurement for online monitoring of parallel stirred-tank bioreactors up to high cell densities. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
6
|
Ultra-high throughput screening for novel protease specificities. Methods Enzymol 2020. [PMID: 32943144 DOI: 10.1016/bs.mie.2020.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The screening of large libraries of enzyme variants remains an essential tool in evolving biocatalysts toward improved properties for applications in medicine, chemistry, and a broad variety of other fields. Over the last decades, the technology for conducting systematic screens of arrayed members of a library of enzyme variants has made great strides in terms of increasing throughput and reducing assay volume. Here, we describe in detail an alternative to arrayed analysis, which is a screen based on density shifts in result of changed enzyme function, which allows highly parallelized screening. Specifically, we link changes in protease substrate specificity in vivo to the production of an alternative reporter protein, catalase. Depending on the catalase expression level, microcolonies of library bacteria with active protease variants contained in polymeric droplets generate an oxygen bubble, which causes a density shift in the droplet and enables it to float.
Collapse
|
7
|
Lindeque RM, Woodley JM. The Effect of Dissolved Oxygen on Kinetics during Continuous Biocatalytic Oxidations. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00140] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Rowan M. Lindeque
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - John M. Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| |
Collapse
|
8
|
Pappenreiter PA, Zwirtmayr S, Mauerhofer LM, Rittmann SKMR, Paulik C. Development of a simultaneous bioreactor system for characterization of gas production kinetics of methanogenic archaea at high pressure. Eng Life Sci 2019; 19:537-544. [PMID: 32625030 PMCID: PMC6999276 DOI: 10.1002/elsc.201900035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/06/2019] [Accepted: 05/22/2019] [Indexed: 11/06/2022] Open
Abstract
Cultivation of methanogens under high pressure offers a great opportunity in biotechnological processes, one of which is the improvement of the gas‐liquid transfer of substrate gases into the medium broth. This article describes a newly developed simultaneous bioreactor system consisting of four identical cultivation vessels suitable for investigation of microbial activity at pressures up to 50 bar and temperatures up to 145°C. Initial pressure studies at 10 and 50 bar of the autotrophic and hydrogenotrophic methanogens Methanothermobacter marburgensis, Methanobacterium palustre, and Methanobacterium thermaggregans were performed to evaluate the reproducibility of the system as well as to test the productivity of these strains. The strains were compared with respect to gas conversion (%), methane evolution rate (MER) (mmol L‐1 h−1), turnover rate (h−1), and maximum conversion rate (kmin) (bar h−1). A pressure drop that can be explained by the reaction stoichiometry showed that all tested strains were active under pressurized conditions. Our study sheds light on the production kinetics of methanogenic strains under high‐pressure conditions. In addition, the simultaneous bioreactor system is a suitable first step screening system for analyzing the substrate uptake and/or production kinetics of gas conversion and/or gas production processes for barophilic or barotolerant microbes.
Collapse
Affiliation(s)
| | - Sara Zwirtmayr
- Institute for Chemical Technology of Organic Materials Johannes Kepler University Linz Linz Austria
| | - Lisa-Maria Mauerhofer
- Archaea Physiology & Biotechnology Group Archaea Biology and Ecogenomics Division Department of Ecogenomics and Systems Biology Universität Wien Wien Austria
| | - Simon Karl-Maria Rasso Rittmann
- Archaea Physiology & Biotechnology Group Archaea Biology and Ecogenomics Division Department of Ecogenomics and Systems Biology Universität Wien Wien Austria
| | - Christian Paulik
- Institute for Chemical Technology of Organic Materials Johannes Kepler University Linz Linz Austria
| |
Collapse
|
9
|
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.
Collapse
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
| | | |
Collapse
|
10
|
Improved microscale cultivation of Pichia pastoris for clonal screening. Fungal Biol Biotechnol 2018; 5:8. [PMID: 29750118 PMCID: PMC5932850 DOI: 10.1186/s40694-018-0053-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/28/2018] [Indexed: 11/10/2022] Open
Abstract
Background Expanding the application of technical enzymes, e.g., in industry and agriculture, commands the acceleration and cost-reduction of bioprocess development. Microplates and shake flasks are massively employed during screenings and early phases of bioprocess development, although major drawbacks such as low oxygen transfer rates are well documented. In recent years, miniaturization and parallelization of stirred and shaken bioreactor concepts have led to the development of novel microbioreactor concepts. They combine high cultivation throughput with reproducibility and scalability, and represent promising tools for bioprocess development. Results Parallelized microplate cultivation of the eukaryotic protein production host Pichia pastoris was applied effectively to support miniaturized phenotyping of clonal libraries in batch as well as fed-batch mode. By tailoring a chemically defined growth medium, we show that growth conditions are scalable from microliter to 0.8 L lab-scale bioreactor batch cultivation with different carbon sources. Thus, the set-up allows for a rapid physiological comparison and preselection of promising clones based on online data and simple offline analytics. This is exemplified by screening a clonal library of P. pastoris constitutively expressing AppA phytase from Escherichia coli. The protocol was further modified to establish carbon-limited conditions by employing enzymatic substrate-release to achieve screening conditions relevant for later protein production processes in fed-batch mode. Conclusion The comparison of clonal rankings under batch and fed-batch-like conditions emphasizes the necessity to perform screenings under process-relevant conditions. Increased biomass and product concentrations achieved after fed-batch microscale cultivation facilitates the selection of top producers. By reducing the demand to conduct laborious and cost-intensive lab-scale bioreactor cultivations during process development, this study will contribute to an accelerated development of protein production processes. Electronic supplementary material The online version of this article (10.1186/s40694-018-0053-6) contains supplementary material, which is available to authorized users.
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
A two-stage biological gas to liquid transfer process to convert carbon dioxide into bioplastic. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.biteb.2018.02.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
13
|
Glauche F, Glazyrina J, Cruz Bournazou MN, Kiesewetter G, Cuda F, Goelling D, Raab A, Lang C, Neubauer P. Detection of growth rate-dependent product formation in miniaturized parallel fed-batch cultivations. Eng Life Sci 2017; 17:1215-1220. [PMID: 32624749 PMCID: PMC6999230 DOI: 10.1002/elsc.201600029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 04/28/2017] [Accepted: 07/24/2017] [Indexed: 12/22/2022] Open
Abstract
Saccharomyces cerevisiae is a popular expression system for recombinant proteins. In most cases, production processes are performed as carbon-limited fed-batch cultures to avoid aerobic ethanol formation. Especially for constitutive expression systems, the specific product formation rate depends on the specific growth rate. The development of optimal feeding strategies strongly depends on laboratory-scale cultivations, which are time and resource consuming, especially when continuous experiments are carried out. It is therefore beneficial for accelerated process development to look at alternatives. In this study, S. cerevisiae AH22 secreting a heterologous endo-polygalacturonase (EPG) was characterized in microwell plates with an enzyme-based fed-batch medium. Through variation of the glucose release rate, different growth profiles were established and the impact on EPG secretion was analyzed. Product formation rates of 200-400 U (gx h)-1 were determined. As a reference, bioreactor experiments using the change-stat cultivation technique were performed. The growth-dependent product formation was analyzed over dilution rates of D = 0.01-0.35 with smooth change of D at a rate of 0.003 h-2. EPG production was found to be comparable with a qp of 400 U (gx h)-1 at D = 0.27 h-1. The presented results indicate that parallel miniaturized fed-batch cultures can be applied to determine product formation profiles of putative production strains. With further automation and parallelization of the concept, strain characterization can be performed in shorter time.
Collapse
Affiliation(s)
- Florian Glauche
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | - Julia Glazyrina
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | | | | | - Fabian Cuda
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| | | | | | | | - Peter Neubauer
- Chair of Bioprocess EngineeringTechnische Universität BerlinBerlinGermany
| |
Collapse
|
14
|
Koepff J, Keller M, Tsolis KC, Busche T, Rückert C, Hamed MB, Anné J, Kalinowski J, Wiechert W, Economou A, Oldiges M. Fast and reliable strain characterization of Streptomyces lividans
through micro-scale cultivation. Biotechnol Bioeng 2017; 114:2011-2022. [DOI: 10.1002/bit.26321] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/15/2017] [Accepted: 04/17/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Joachim Koepff
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology; Leo-Brandt-Straße 52428 Jülich Germany
| | - Matthias Keller
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology; Leo-Brandt-Straße 52428 Jülich Germany
| | - Konstantinos C. Tsolis
- Laboratory of Molecular Bacteriology; Department of Microbiology and Immunology; Rega Institute for Medical Research; KU Leuven-University of Leuven; Leuven Belgium
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld University; Bielefeld Germany
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld University; Bielefeld Germany
| | - Mohamed B. Hamed
- Laboratory of Molecular Bacteriology; Department of Microbiology and Immunology; Rega Institute for Medical Research; KU Leuven-University of Leuven; Leuven Belgium
- Department of Molecular Biology Department; The National Research Centre, Dokki; Giza Egypt
| | - Jozef Anné
- Laboratory of Molecular Bacteriology; Department of Microbiology and Immunology; Rega Institute for Medical Research; KU Leuven-University of Leuven; Leuven Belgium
| | - Joern Kalinowski
- Center for Biotechnology (CeBiTec), Microbial Genomics and Biotechnology; Bielefeld University; Bielefeld Germany
| | - Wolfgang Wiechert
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology; Leo-Brandt-Straße 52428 Jülich Germany
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology; Department of Microbiology and Immunology; Rega Institute for Medical Research; KU Leuven-University of Leuven; Leuven Belgium
| | - Marco Oldiges
- Forschungszentrum Jülich GmbH; Institute of Bio- and Geosciences; IBG-1: Biotechnology; Leo-Brandt-Straße 52428 Jülich Germany
- Institute of Biotechnology; RWTH Aachen University; Worringer Weg 3 52074 Aachen Germany
| |
Collapse
|
15
|
Gravity-Driven Adaptive Evolution of an Industrial Brewer’s Yeast Strain towards a Snowflake Phenotype in a 3D-Printed Mini Tower Fermentor. FERMENTATION-BASEL 2017. [DOI: 10.3390/fermentation3010004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
16
|
Meo A, Priebe XL, Weuster-Botz D. Lipid production with Trichosporon oleaginosus in a membrane bioreactor using microalgae hydrolysate. J Biotechnol 2017; 241:1-10. [DOI: 10.1016/j.jbiotec.2016.10.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/19/2016] [Accepted: 10/24/2016] [Indexed: 11/26/2022]
|
17
|
Wellenbeck W, Mampel J, Naumer C, Knepper A, Neubauer P. Fast-track development of a lactase production process with Kluyveromyces lactis by a progressive parameter-control workflow. Eng Life Sci 2016; 17:1185-1194. [PMID: 32624746 DOI: 10.1002/elsc.201600031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 08/12/2016] [Accepted: 09/07/2016] [Indexed: 11/12/2022] Open
Abstract
The time-to-market challenge is key to success for consumer goods affiliated industries. In recent years, the dairy industry faces a fast and constantly growing demand for enzymatically produced lactose-free milk products, mainly driven by emerging markets in South America and Asia. In order to take advantage of this opportunity, we developed a fermentation process for lactase (β-galactosidase) from Kluyveromyces lactis within short time. Here, we describe the process of stepwise increasing the level of control over relevant process parameters during scale-up that established a highly efficient and stable production system. Process development started with evolutionary engineering to generate catabolite-derepressed variants of the K. lactis wild-type strain. A high-throughput screening mimicking fed-batch cultivation identified a constitutive lactase overproducer with 260-fold improved activity of 4.4 U per milligram dry cell weight when cultivated in glucose minimal medium. During scale-up, process control was progressively increased up to the level of conventional, fully controlled fed-batch cultivations by simulating glucose feed, applying pH- and dissolved oxygen tension (DOT)-sensor technology to small scale, and by the use of a milliliter stirred tank bioreactor. Additionally, process development was assisted by design-of-experiments optimization of the growth medium employing the response surface methodology.
Collapse
Affiliation(s)
- Wenzel Wellenbeck
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany
| | - Jörg Mampel
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany
| | - Christian Naumer
- BRAIN AG (Biotechnology Research and Information Network) Zwingenberg Germany
| | - Andreas Knepper
- Bioprocess Engineering Department of Biotechnology Technische Universität Berlin Berlin Germany
| | - Peter Neubauer
- Bioprocess Engineering Department of Biotechnology Technische Universität Berlin Berlin Germany
| |
Collapse
|
18
|
Schmideder A, Hensler S, Lang M, Stratmann A, Giesecke U, Weuster-Botz D. High-cell-density cultivation and recombinant protein production with Komagataella pastoris in stirred-tank bioreactors from milliliter to cubic meter scale. Process Biochem 2016. [DOI: 10.1016/j.procbio.2015.11.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
19
|
Poschenrieder ST, Wagner SG, Castiglione K. Efficient production of uniform nanometer-sized polymer vesicles in stirred-tank reactors. J Appl Polym Sci 2015. [DOI: 10.1002/app.43274] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sarah Theresa Poschenrieder
- Institute of Biochemical Engineering; Technische Universität München; Boltzmannstraße 15 Garching D-85748 Germany
| | - Sabine Gabriele Wagner
- Institute of Biochemical Engineering; Technische Universität München; Boltzmannstraße 15 Garching D-85748 Germany
| | - Kathrin Castiglione
- Institute of Biochemical Engineering; Technische Universität München; Boltzmannstraße 15 Garching D-85748 Germany
| |
Collapse
|
20
|
Janzen NH, Schmidt M, Krause C, Weuster-Botz D. Evaluation of fluorimetric pH sensors for bioprocess monitoring at low pH. Bioprocess Biosyst Eng 2015; 38:1685-92. [PMID: 25969385 DOI: 10.1007/s00449-015-1409-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/28/2015] [Indexed: 12/24/2022]
Abstract
Optical chemical sensors are the standard for pH monitoring in small-scale bioreactors such as microtiter plates, shaking flasks or other single-use bioreactors. The dynamic pH range of the so far commercially available fluorescent pH sensors applied in small-scale bioreactors is restricted to pH monitoring around neutral pH, although many fermentation processes are performed at pH < 6 on industrial scale. Thus, two new prototype acidic fluorescence pH sensors immobilized in single-use stirred-tank bioreactors, one with excitation at 470 nm and emission at 550 nm (sensor 470/550) and the other with excitation at 505 nm and emission at 600 nm (sensor 505/600), were characterized with respect to dynamic ranges and operational stability in representative fermentation media. Best resolution and dynamic range was observed with pH sensor 505/600 in mineral medium (dynamic range of 3.9 < pH < 7.2). Applying the same pH sensors to complex medium results in a drastic reduction of resolution and dynamic ranges. Yeast extract in complex medium was found to cause background fluorescence at the sensors' operating wavelength combinations. Optical isolation of the sensor by adding a black colored polymer layer above the sensor spot and fixing an aperture made of adhesive photoresistant foil between the fluorescence reader and the transparent bottom of the polystyrene reactors enabled full re-establishment of the sensor's characteristics. Reliability and operational stability of sensor 505/600 was shown by online pH monitoring (4.5 < pH < 5.8) of parallel anaerobic batch fermentations of Clostridium acetobutylicum for the production of acetone, butanol and ethanol (ABE) with offline pH measurements with a standard glass electrode as reference.
Collapse
Affiliation(s)
- Nils H Janzen
- Lehrstuhl für Bioverfahrenstechnik, Technische Universität München, Boltzmannstr. 15, 85748, Garching, Germany,
| | | | | | | |
Collapse
|
21
|
Faust G, Janzen NH, Bendig C, Römer L, Kaufmann K, Weuster-Botz D. Feeding strategies enhance high cell density cultivation and protein expression in milliliter scale bioreactors. Biotechnol J 2014; 9:1293-303. [DOI: 10.1002/biot.201400346] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/18/2014] [Accepted: 08/05/2014] [Indexed: 12/23/2022]
|
22
|
Käß F, Prasad A, Tillack J, Moch M, Giese H, Büchs J, Wiechert W, Oldiges M. Rapid assessment of oxygen transfer impact for Corynebacterium glutamicum. Bioprocess Biosyst Eng 2014; 37:2567-77. [DOI: 10.1007/s00449-014-1234-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/02/2014] [Indexed: 10/25/2022]
|
23
|
Formenti LR, Nørregaard A, Bolic A, Hernandez DQ, Hagemann T, Heins AL, Larsson H, Mears L, Mauricio-Iglesias M, Krühne U, Gernaey KV. Challenges in industrial fermentation technology research. Biotechnol J 2014; 9:727-38. [PMID: 24846823 DOI: 10.1002/biot.201300236] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/01/2014] [Accepted: 04/23/2014] [Indexed: 11/06/2022]
Abstract
Industrial fermentation processes are increasingly popular, and are considered an important technological asset for reducing our dependence on chemicals and products produced from fossil fuels. However, despite their increasing popularity, fermentation processes have not yet reached the same maturity as traditional chemical processes, particularly when it comes to using engineering tools such as mathematical models and optimization techniques. This perspective starts with a brief overview of these engineering tools. However, the main focus is on a description of some of the most important engineering challenges: scaling up and scaling down fermentation processes, the influence of morphology on broth rheology and mass transfer, and establishing novel sensors to measure and control insightful process parameters. The greatest emphasis is on the challenges posed by filamentous fungi, because of their wide applications as cell factories and therefore their relevance in a White Biotechnology context. Computational fluid dynamics (CFD) is introduced as a promising tool that can be used to support the scaling up and scaling down of bioreactors, and for studying mixing and the potential occurrence of gradients in a tank.
Collapse
Affiliation(s)
- Luca Riccardo Formenti
- Department of Chemical and Biochemical Engineering, Technical University of Denmark (DTU), Lyngby, Denmark
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Nunes MAP, Fernandes PCB, Ribeiro MHL. Microtiter plates versus stirred mini-bioreactors in biocatalysis: a scalable approach. BIORESOURCE TECHNOLOGY 2013; 136:30-40. [PMID: 23563437 DOI: 10.1016/j.biortech.2013.02.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 02/10/2013] [Accepted: 02/20/2013] [Indexed: 06/02/2023]
Abstract
To place the application of miniaturized vessels as microbioreactors on a firm footing, focus has been given to engineering characterization. Studies on this matter have mostly involved carrier-free biological systems, while support-based systems have been overlooked. The present work aims to contribute to fill in such gap. Thus, it intended to establish a robust scaled down approach to identify and optimize relevant operational conditions of naringin hydrolysis by naringinase in PVA lens-shaped particles. The influence of geometric and dynamic (viz. Reynolds number) parameters was evaluated. Naringin hydrolysis in round, flat bottom MTP proved more effective than in square, pyramidal bottom. The bioconversion at MTP and stirred tank reactors scales showed that, given the 12.5-fold scale difference was in agreement between the bioconversion rates. The external mass transfer resistances were negligible as deduced from Damkohler modulus ≤1. The bioconversion was effectively scaled-up 200-fold from shaken microtiter plates to stirred tank reactors.
Collapse
Affiliation(s)
- Mário A P Nunes
- Research Institute for Medicines and Pharmaceutical Sciences (i-Med-UL), Faculdade de Farmácia, University of Lisbon, Av., Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | | | | |
Collapse
|
25
|
Demming S, Peterat G, Llobera A, Schmolke H, Bruns A, Kohlstedt M, Al-Halhouli A, Klages CP, Krull R, Büttgenbach S. Vertical microbubble column-A photonic lab-on-chip for cultivation and online analysis of yeast cell cultures. BIOMICROFLUIDICS 2012; 6:34106. [PMID: 23882299 PMCID: PMC3416849 DOI: 10.1063/1.4738587] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 07/03/2012] [Indexed: 05/11/2023]
Abstract
This paper presents a vertically positioned microfluidic system made of poly(dimethylsiloxane) (PDMS) and glass, which can be applied as a microbubble column (μBC) for biotechnological screening in suspension. In this μBC, microbubbles are produced in a cultivation chamber through an integrated nozzle structure. Thus, homogeneous suspension of biomass is achieved in the cultivation chamber without requiring additional mixing elements. Moreover, blockage due to produced carbon dioxide by the microorganisms-a problem predominant in common, horizontally positioned microbioreactors (MBRs)-is avoided, as the gas bubbles are released by buoyancy at the upper part of the microsystem. The patterned PDMS layer is based on an optimized two-lithographic process. Since the naturally hydrophobic PDMS causes problems for the sufficient production of microbubbles, a method based on polyelectrolyte multilayers is applied in order to allow continuous hydrophilization of the already bonded PDMS-glass-system. The μBC comprises various microelements, including stabilization of temperature, control of continuous bubble formation, and two optical configurations for measurement of optical density with two different sensitivities. In addition, the simple and robust application and handling of the μBC is achieved via a custom-made modular plug-in adapter. To validate the scalability from laboratory scale to microscale, and thus to demonstrate the successful application of the μBC as a screening instrument, a batch cultivation of Saccharomyces cerevisiae is performed in the μBC and compared to shake flask cultivation. Monitoring of the biomass growth in the μBC with the integrated online analytics resulted in a specific growth rate of 0.32 h(-1), which is almost identical to the one achieved in the shake flask cultivation (0.31 h(-1)). Therefore, the validity of the μBC as an alternative screening tool compared to other conventional laboratory scale systems in bioprocess development is proven. In addition, vertically positioned microbioreactors show high potential in comparison to conventional screening tools, since they allow for high density of integrated online analytics and therefore minimize time and cost for screening and guarantee improved control and analysis of cultivation parameters.
Collapse
Affiliation(s)
- Stefanie Demming
- Institut für Mikrotechnik, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Klein T, Schneider K, Heinzle E. A system of miniaturized stirred bioreactors for parallel continuous cultivation of yeast with online measurement of dissolved oxygen and off-gas. Biotechnol Bioeng 2012; 110:535-42. [DOI: 10.1002/bit.24633] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 07/24/2012] [Accepted: 07/25/2012] [Indexed: 11/10/2022]
|
27
|
Soley A, Fontova A, Gálvez J, Sarró E, Lecina M, Bragós R, Cairó J, Gòdia F. Development of a simple disposable six minibioreactor system for suspension mammalian cell culture. Process Biochem 2012. [DOI: 10.1016/j.procbio.2011.12.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
28
|
Glucose-limited high cell density cultivations from small to pilot plant scale using an enzyme-controlled glucose delivery system. N Biotechnol 2012; 29:235-42. [DOI: 10.1016/j.nbt.2011.11.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 10/07/2011] [Accepted: 11/02/2011] [Indexed: 11/22/2022]
|
29
|
Hortsch R, Krispin H, Weuster-Botz D. Process performance of parallel bioreactors for batch cultivation of Streptomyces tendae. Bioprocess Biosyst Eng 2010; 34:297-304. [DOI: 10.1007/s00449-010-0471-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 09/21/2010] [Indexed: 11/24/2022]
|