Microlitre/millilitre shaken bioreactors in fermentative and biotransformation processes – a review

References

• Amanullah A, McFarlane CM, Emery AN, Nienow AW. Scale-down model to simulate spatial pH variations in large-scale bioreactors. Biotechnol Bioeng 2001; 73: 390–399
   PubMed Web of Science ®Google Scholar
• Anderlei T, Büchs J. Device for sterile online measurement of the oxygen transfer rate in shaking flasks. Biochem Eng J 2001; 7: 157–162
   PubMed Web of Science ®Google Scholar
• Anderlei T, Zang W, Papaspyrou M, Büchs J. Online respiration activity measurement (OTR, CTR, RQ) in shake flasks. Biochem Eng J 2004; 17: 187–194
   Web of Science ®Google Scholar
• Balmer GJ, Moore IPT, Nienow CM. Aerated and unaerated power and mass transfer characteristics of Prochem agitators. Biotechnology Processes Scale-up and Mixing, CS Ho, JY Oldshue. American Institute of Chemical Engineers, New York 1987; 116–127
   Google Scholar
• Baminger U, Ludwig R, Galhaup C, Leitner C, Kulbe KD, Haltrich D. Continuous enzymatic regeneration of redox mediators used in biotransformation reactions employing flavoproteins. J Molec Catal B: Enzym 2001; 11: 541–550
   Google Scholar
• Berg M, Undisz K, Thiericke R, Zimmermann P, Moore T, Posten C. Evaluation of liquid handling conditions in microplates. J Biomol Screen 2001; 6: 47–56
   PubMedGoogle Scholar
• Boettner M, Prinz B, Holz C, Stahl U, Lang C. High-throughput screening for expression of heterologous proteins in the yeast Pichia pastoris. J Biotechnol 2002; 99: 51–62
   PubMed Web of Science ®Google Scholar
• Bornscheuer UT, Pohl M. Improved biocatalysts by directed evolution and rational protein design. Curr Opin Chem Biol 2001; 5: 137–143
   PubMed Web of Science ®Google Scholar
• Brunati M, Marinelli F, Bertolini C, Gandolfi R, Daffonchio D, Molinari F. Biotransformations of cinnamic and ferulic acid with actinomycetes. Enzym Microb Technol 2004; 34: 3–9
   Google Scholar
• Büchs J, Maier U, Milbradt C, Zoels B. Power consumption in shaking flasks on rotary shaking machines: I. power consumption measurement in unbaffled flasks at low liquid viscosity. Biotechnol Bioeng 2000a; 68: 589–593
   PubMed Web of Science ®Google Scholar
• Büchs J, Maier U, Milbradt C, Zoels B. Power consumption in shaking flasks on rotary shaking machines, part II: non-dimensional description of the specific power consumption and flow-regimes in unbaffled flasks at elevated liquid viscosity. Biotechnol Bioeng 2000b; 68: 594–601
   PubMed Web of Science ®Google Scholar
• Büchs J. Introduction to advantages and problems of shaken cultures. Biochem Eng J 2001; 7: 91–98
   PubMed Web of Science ®Google Scholar
• Büchs J, Lotter S, Milbradt C. Out-of-phase operating conditions, a hitherto unknown phenomenon in shaken bioreactors. Biochem Eng J 2001; 7: 135–141
   PubMedGoogle Scholar
• Burbaum JJ. Miniaturization technologies in HTS: how fast, how small, how soon?. Drug Discovery Today 1998; 3: 313–322
   Google Scholar
• Casey JT, O'Cleirigh C, Walsh PK, O'Shea DG. Development of a robust microtiter plate-based assay method for assessment of bioactivity. J Microbiol Meth 2004; 58: 327–334
   PubMed Web of Science ®Google Scholar
• Chisti Y, Jauregui-Haza UJ. Oxygen transfer and mixing in mechanically agitated airlift bioreactors. Biochem Eng J 2002; 10: 143–153
   Web of Science ®Google Scholar
• Danielson PB, Büchs J, Stöckmann C, Fogleman JC. Maximizing cell densities in miniprep-scale cultures with H15 medium and improved oxygen transfer. Biochem Eng J 2004; 17: 175–180
   Google Scholar
• Doig SD, Pickering SR, Lye GJ, Woodley JM. The use of microscale processing techniques for quantification of biocatalytic Baeyer–Villiger oxidation kinetics. Biotechnol Bioeng 2002; 80: 42–49
   PubMed Web of Science ®Google Scholar
• Doig SD, Diep A, Baganz F. Characterisation of a novel miniaturised bubble column bioreactor for high throughput cell cultivation. Biochem Eng J 2005a; 23: 97–105
   Web of Science ®Google Scholar
• Doig SD, Pickering SCR, Lye GJ, Baganz F. Modelling surface aeration rates in shaken microtitre plates using dimensionless groups. Chem Eng Sci 2005b; 60: 2741–2750
   Google Scholar
• Duetz WA, Rüedi L, Hermann R, O'Connor K, Büchs J, Witholt B. Methods for intense aeration, growth, storage, and replication of bacterial strains in microtiter plates. Appl Environ Microbiol 2000; 66: 2641–2646
   PubMed Web of Science ®Google Scholar
• Duetz WA, Witholt B. Effectiveness of orbital shaking for the aeration of suspended bacterial cultures in square deepwell microtiter plates. Biochem Eng J 2001; 7: 113–115
   PubMed Web of Science ®Google Scholar
• Duetz WA, Witholt B. Oxygen transfer by orbital shaking of square vessels and deepwell microtiter plates of various dimensions. Biochem Eng J 2004; 17: 181–185
   Google Scholar
• Eliezer ED. Power absorption by new and hybrid mixing systems under gassed and ungassed conditions. Biotechnology Processes Scale-up and Mixing, CS Ho, JY Oldshue. American Institute of Chemical Engineers, New York 1987; 22–30
   Google Scholar
• Elmahdi I, Baganz F, Dixon K, Harrop T, Sugden D, Lye GJ. pH control in microwell fermentations of S. erythraea CA340: influence on biomass growth kinetics and erythromycin biosynthesis. Biochem Eng J 2003; 16: 299–310
   Google Scholar
• Freyer SA, König M, Künkel A. Validating shaking flasks as representative screening systems. Biochem Eng J 2004; 17: 169–173
   Google Scholar
• Gaden EL. Improved shaken flask performance. Biotechnol Bioeng 1962; 4: 99–103
   Google Scholar
• Gbewonyo K, Dimasi D, Buckland BC. Characterization of oxygen transfer and power absorption of hydrofoil impellers in viscous mycelial fermentations. Biotechnology Processes Scale-up and Mixing, CS Ho, JY. Oldshue. American Institute of Chemical Engineers, New York 1987; 128–134
   Google Scholar
• Gerlach SR, Siedenberg D, Gerlach D, Schügerl K, Giuseppin MLF, Hunik J. Influence of reactor systems on the morphology of Aspergillus awamori. Application of neural network and cluster analysis for characterization of fungal morphology. Process Biochem 1998; 33: 601–615
   Google Scholar
• Girard P, Jordan M, Tsao M, Wurm FM. Small-scale bioreactor system for process development and optimization. Biochem Eng J 2001; 7: 117–119
   PubMed Web of Science ®Google Scholar
• Gupta A, Rao G. A study of oxygen transfer in shake flasks using a non-invasive oxygen sensor. Biotechnol Bioeng 2003; 84: 351–358
   PubMedGoogle Scholar
• Heisler I, Keller J, Tauber R, Sutherland M, Fuchs H. A colorimetric assay for the quantitation of free adenine applied to determine the enzymatic activity of ribosome-inactivating proteins. Anal Biochem 2002; 302: 114–122
   PubMed Web of Science ®Google Scholar
• Henzler H-J, Schedel M. Suitability of shaking flasks for oxygen supply to microbial cultures. Bioprocess Eng 1991; 7: 123–131
   Google Scholar
• Hermann R, Walther N, Maier U, Büchs J. Optical method for the determination of the oxygen-transfer capacity of small bioreactors based on sulfite oxidation. Biotechnol Bioeng 2001; 74: 355–363
   PubMedGoogle Scholar
• Hermann R, Lehmann M, Büchs J. Characterization of gas-liquid mass transfer phenomena in microtiter plates. Biotechnol Bioeng 2003; 81: 178–186
   PubMed Web of Science ®Google Scholar
• Hertzberg RP, Pope AJ. High-throughput screening: new technology for the 21st century. Curr Opin Chem Biol 2000; 4: 445–451
   PubMed Web of Science ®Google Scholar
• Ho CS, Ju L-K. Effects of microorganisms on effective oxygen diffusion coefficients and solubilities in fermentation media. Biotechnol Bioeng 1988; 32: 313–325
   PubMedGoogle Scholar
• Jansen M, Veurink JH, Euverink G-JW, Dijkhuizen L. Growth of the salt-tolerant yeast Zygosaccharomyces rouxii in microtiter plates: effects of NaCl, pH and temperature on growth and fusel alcohol production from branched-chain amino acids. FEMS Yeast Res 2003; 3: 313–318
   PubMed Web of Science ®Google Scholar
• John GT, Heinzle E. Quantitative screening method for hydrolases in microplates using pH indicators: determination of kinetic parameters by dynamic pH monitoring. Biotechnol Bioeng 2001; 72: 620–627
   PubMedGoogle Scholar
• John GT, Klimant I, Wittmann C, Heinzle E. Integrated optical sensing of dissolved oxygen in microtiter plates: A novel tool for microbial cultivation. Biotechnol Bioeng 2003; 81: 829–836
   PubMed Web of Science ®Google Scholar
• Junker BH. Scale-up methodologies for Escherichia coli and yeast fermentation processes. J Biosci Bioeng 2004; 97: 347–364
   PubMed Web of Science ®Google Scholar
• Kato I, Tanaka H. Development of novel box-shaped shake flask with efficient gas exchange capacity. J Ferment Bioeng 1998; 85: 404–409
   Google Scholar
• Katzer W, Blackburn M, Charman K, Martin S, Penn J, Wrigley S. Scale-up of filamentous organisms from tubes and shake-flasks into stirred vessels. Biochem Eng J 2001; 7: 127–134
   PubMedGoogle Scholar
• Kensy F, Zimmermann HF, Knabben I, Anderlei T, Trauthwein H, Dingerdissen U, Büchs J. Oxygen transfer phenomena in 48-well microtiter plates: Determination by optical monitoring of sulfite oxidation and verification by real-time measurement during microbial growth. Biotechnol Bioeng 2005; 89: 698–708
   PubMed Web of Science ®Google Scholar
• Klimant I, Wolfbeis OS. Oxygen-sensitive luminescent materials based on silicone-soluble ruthenium diimine complexes. Anal Chem 1995; 67: 3160–3166
   Google Scholar
• Kulmala S, Suomi J. Current status of modern analytical luminescence methods. Analytica Chimica Acta 2003; 500: 21–69
   Web of Science ®Google Scholar
• Kumar S, Wittmann C, Heinzle E. Minibioreactors. Biotechnol Lett 2004; 26: 1–10
   PubMed Web of Science ®Google Scholar
• Lafferty, M. 2002. GigaMatrix holding tray having through-hole wells. US Patent US2002080350.
   Google Scholar
• Lamping SR, Zhang H, Allen B, Shamlou PA. Design of a prototype miniature bioreactor for high throughput automated bioprocessing. Chem Eng Sci 2003; 58: 747–758
   Web of Science ®Google Scholar
• Langheinrich C, Nienow AW. Control of pH in large-scale, free suspension animal cell bioreactors: alkali addition and pH excursions. Biotechnol Bioeng 1999; 66: 171–179
   PubMed Web of Science ®Google Scholar
• Leach M. Marvelous microplates. Drug Discov Today 1997; 2: 174–175
   Google Scholar
• Leib TM, Pereira CJ, Villadsen J. Bioreactors: a chemical engineering perspective. Chem Eng Sci 2001; 56: 5485–5497
   Google Scholar
• Losen M, Frölich B, Pohl M, Büchs J. Effect of oxygen limitation and medium composition on Escherichia coli fermentation in shake-flask cultures. Biotechnol Prog 2004; 20: 1062–1068
   PubMedGoogle Scholar
• Lotter S, Büchs J. Utilization of specific power input measurements for optimization of culture conditions in shaking flasks. Biochem Eng J 2004; 17: 195–203
   Google Scholar
• Lye GJ, Ayazi-Shamlou P, Baganz F, Dalby PA, Woodley JM. Accelerated design of bioconversion processes using automated microscale processing techniques. Trends Biotechnol 2003; 21: 29–37
   PubMedGoogle Scholar
• Maier U, Büchs J. Characterisation of the gas-liquid mass transfer in shaking bioreactors. Biochem Eng J 2001; 7: 99–106
   PubMedGoogle Scholar
• May O, Nguyen PT, Arnold FH. Inverting enantioselectivity by directed evolution of hydantoinase for improved production of L-methionine. Nat Biotechnol 2000; 18: 317–320
   PubMed Web of Science ®Google Scholar
• McDaniel LE, Bailey EG, Zimmerli A. Effect of oxygen supply rates on growth of Escherichia coli. I. Studies in unbaffled and baffled shake flasks. Appl Microbiol 1965; 13: 100–114
   Google Scholar
• Miled N, Beisson F, de Caro J, de Caro A, Arondel V, Verger R. Interfacial catalysis by lipases. J Molec Cataly B: Enzym 2001; 11: 165–171
   Google Scholar
• Mrotzek C, Anderlei T, Henzler H-J, Büchs J. Mass transfer resistance of sterile plugs in shaking bioreactors. Biochem Eng J 2001; 7: 107–112
   PubMedGoogle Scholar
• Nakayama GRI. Microplate assays for high-throughput screening. Curr Opin Drug Discov Develop 1998; 1: 85–91
   PubMedGoogle Scholar
• Nielsen JH, Villadsen J, Liden G. Bioreaction Engineering Principles2nd edition. Kluwer Academic Publishers, New York 2002
   Google Scholar
• Nienow AW. Hydrodynamics of stirred bioreactors. Appl Mech Rev 1998; 51: 3–32
   Google Scholar
• Oldenburg KR, Zhang JH, Chen TM, Maffia A, Blom KF, Combs AP, Chung TDY. Assay miniaturization for ultra-high throughput screening of combinatorial and discrete compound libraries – A 9600-well (0.2 microliter) assay system. J Biomol Screen 1998; 3: 55–62
   Web of Science ®Google Scholar
• Oliveira R, Clemente JJ, Cunha AE, Carrondo MJT. Adaptive dissolved oxygen control through the glycerol feeding in a recombinant Pichia pastoris cultivation in conditions of oxygen transfer limitation. J Biotechnol 2005; 116: 35–50
   PubMedGoogle Scholar
• Peter CP, Lotter S, Maier U, Büchs J. Impact of out-of-phase conditions on screening results in shaking flask experiments. Biochem Eng J 2004; 17: 205–215
   Google Scholar
• Rainer BW. Determination methods of the volumetric oxygen transfer coefficient kLa in bioreactors. Chem Biochem Eng 1990; 4: 185–196
   Google Scholar
• Reeves AR., Cernota WH, Brikun IA, Wesley RK, Weber JM. Engineering precursor flow for increased erythromycin production in Aeromicrobium erythreum. Metabolic Eng 2004; 6: 300–312
   PubMedGoogle Scholar
• Reyes C, Peña C, Galindo E. Reproducing shake flasks performance in stirred fermentors: production of alginates by Azotobacter vinelandii. J Biotechnol 2003; 105: 189–198
   PubMedGoogle Scholar
• Robertson DE, Steer BA. Recent progress in biocatalyst discovery and optimization. Curr Opin Chem Biol 2004; 8: 141–149
   PubMedGoogle Scholar
• Schmidt-Dannert C, Umeno D, Arnold FH. Molecular breeding of carotenoid biosynthetic pathways. Nat Biotechnol 2000; 18: 750–753
   PubMed Web of Science ®Google Scholar
• Silberbach M, Maier B, Zimmermann M, Büchs J. Glucose oxidation by Gluconobacter oxydans: characterization in shaking-flasks, scale-up and optimization of the pH profile. Appl Microbiol Biotechnol 2003; 62: 92–98
   PubMed Web of Science ®Google Scholar
• Snape JB, Thomas NH, Callow JA. How suspension cultures of Catharantus roseus respond to oxygen limitation: small-scale tests with applications to large-scale cultures. Biotechnol Bioeng 1989; 34: 1058–1062
   PubMedGoogle Scholar
• Stahl S, Greasham R, Chartrain M. Implementation of a rapid microbial screening procedure for biotransformation activities. J Biosci Bioeng 2000; 89: 367–371
   PubMedGoogle Scholar
• Stöckmann C, Losen M, Dahlems U, Knocke C, Gellissen G, Büchs J. Effect of oxygen supply on passaging, stabilising and screening of recombinant Hansenula polymorpha production strains in test tube cultures. FEMS Yeast Res 2003a; 4: 195–205
   PubMedGoogle Scholar
• Stöckmann C, Maier U, Anderlei T, Knocke C, Gellissen G, Büchs J. The oxygen transfer rate as key parameter for the characterization of Hansenula polymorpha screening cultures. J Ind Microbiol Biotechnol 2003b; 30: 613–622
   PubMedGoogle Scholar
• Sumino Y, Akiyama S, Fukada H. Performance of the shaking flask. I. Power consumption. J Ferment Technol 1972; 50: 203–208
   Google Scholar
• Suzuki S, Taketani H, Kusumoto KI, Kashiwagy Y. High-Throughput Screening for isolation of enhanced green fluorescent protein expressing transformants of filamentous fungus using an image analyzer. J Biosci Bioeng 2003; 96: 313–316
   PubMedGoogle Scholar
• Thiry M, Cingolani D. Optimizing scale-up fermentation processes. Trends Biotechnol 2002; 20: 103–105
   PubMedGoogle Scholar
• Tolosa L, Kostov Y, Harms P, Rao G. Noninvasive measurement of dissolved oxygen in shake flasks. Biotechnol Bioeng 2002; 80: 594–597
   PubMedGoogle Scholar
• Tunac JB. High aeration capacity shake-flask systems. J Ferment Bioeng 1989; 68: 157–159
   Google Scholar
• Van't Riet K. Review of measuring methods and results in nonviscous gas–liquid mass transfer in stirred vessels. Ind Eng Chem Proc Design Develop 1979; 18: 357–364
   Web of Science ®Google Scholar
• Verschuren PG, Cardona TD, Nout MJR, De Gooijer KD, van den Heuvel JC. Location and limitation of cellulose production by Acetobacter xylinum established from oxygen profiles. J Biosci Bioeng 2000; 89: 414–419
   PubMed Web of Science ®Google Scholar
• Wahler D, Reymond J-L. Novel methods for biocatalyst screening. Curr Opin Chem Biol 2001; 5: 152–158
   Google Scholar
• Weis R, Poechlauer P, Bona R, Skranc W, Luiten R, Wubbolts M, Schwab H, Glieder A. Biocatalytic conversion of unnatural substrates by recombinant almond R-HNL isoenzyme 5. J Molec Catal B: Enzym 2004a; 29: 211–218
   Google Scholar
• Weis R, Luiten R, Skranc W, Schwab H, Wubbolts M, Glieder A. Reliable high-throughput screening with Pichia pastoris by limiting yeast cell death phenomena. FEMS Yeast Res 2004b; 5: 179–189
   Google Scholar
• Weisenberger S, Schumpe A. Estimation of gas solubilities in salt solutions at temperatures from 273 K to 363 K. AIChE J 1996; 42: 298–300
   Web of Science ®Google Scholar
• Weuster-Botz D, Altenbach-Rehm J, Arnold M. Parallel substrate feeding and pH-control in shaking flasks. Biochem Eng J 2001; 7: 163–170
   PubMed Web of Science ®Google Scholar
• Wittmann C, Kim HM, John G, Heinzle E. Characterization and application of an optical sensor for quantification of dissolved O2 in shake-flasks. Biotechnol Lett 2003; 25: 377–380
   PubMedGoogle Scholar
• Wölcke J, Ullmann D. Miniaturized HTS technologies – uHTS. Drug Discov Today 2001; 6: 637–646
   PubMed Web of Science ®Google Scholar