Using an Advanced Microfermentor System for Strain Screening and Fermentation Optimization

  • Dongming XieEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 834)


Industrial biotechnology employs microorganisms (strains) for manufacture of certain food or industrial products to meet the increasing need of the world. To develop a bioproduction process, the first step is to screen out a production strain from isolated, mutated, or genetically engineered strain candidates. To maximize the bioproduction of a selected strain, bioreaction (fermentation) conditions need to be optimized. Fermentation experiments in shake flasks, bench-scale fermentors, or a combination of both are the conventional methods for both strain screening and fermentation optimization. Shake-flask experiments are easy to handle and cost-effective compared to experiments in fermentors, but the lower controllability makes the shake-flask data less informative for fermentation scale-up. Bench-scale fermentor experiments (>0.5 L) are well controlled under designed conditions and provide high-quality data, but they are also very time- and cost-consuming. The novel microfermentor system (typically <100 mL), or mentioned as microbioreactor, mini-fermentor, mini-bioreactor, or miniature bioreactor, combines the advantages of both shake-flask’s easy handling and bench-scale fermentor’s controllability, thus can achieve comparable results from fermentors at much higher efficiency and lower cost. This chapter introduces an example of how to use a microfermentor system for strain screening and fermentation optimization.

Key words

Industrial biotechnology Fermentation Microfermentor Microbioreactor Strain screening Optimization 



The author would like to thank Dr. Bjorn D. Tyreus from DuPont Central Research and Development for his review and suggestions.


  1. 1.
    Michael J. Waites, Neil L. Morgan, John S. Rockey, and Gary Higton (2001) Industrial microbiology: an introduction. Wiley-Blackwell.Google Scholar
  2. 2.
    Schäpper D., Alam M.N.H.Z., Szita N., and Lantz A.E., and Gernaey K.V. (2009) Application of microbioreactors in fermentation process development: a review. Anal Bioanal Chem 395, 679–695.PubMedCrossRefGoogle Scholar
  3. 3.
    Weuster-Botz D., Hekmat D., Puskeiler R., and Franco-Lara E. (2007) Enabling Technologies: Fermentation and Downstream Processing. Adv Biochem Eng Biotechnol 105, 205–247.PubMedGoogle Scholar
  4. 4.
    Kumar S., Wittmann C., and Heinzle E. (2004) Minibioreactors. Biotechnology Letters 26, 1–10.PubMedCrossRefGoogle Scholar
  5. 5.
    Jonathan I Betts and Frank Baganz (2006) Miniature bioreactors: current practices and future opportunities. Microbial Cell Factories 5, 21.Google Scholar
  6. 6.
    Fernandes P. and Cabral J.M.S. (2006) Microlitre/millilitre shaken bioreactors in fermentative and biotransformation processes—A review. Biocatal Biotransformation 24, 237–252.CrossRefGoogle Scholar
  7. 7.
    Büchs J. (2001) Introduction to advantages and problems of shaken cultures. Biochem Eng J 7, 91–98.PubMedCrossRefGoogle Scholar
  8. 8.
    Anderlei T., Büchs J. (2001) Device for sterile online measurement of the oxygen transfer rate in shaking flasks. Biochem Eng J 7,157–162.PubMedCrossRefGoogle Scholar
  9. 9.
    Wittmann C., Kim H.M., John G., Heinzle E. (2003) Characterisation and application of an optical sensor for quantification of dissolved oxygen in shake-flasks. Biotechnol Lett 25, 377–380.PubMedCrossRefGoogle Scholar
  10. 10.
    Danielson P.B., Büchs J., Stockmann C., Fogleman J.C. (2004) Maximizing cell densities in miniprep-scale cultures with H15 medium and improved oxygen transfer. Biochem Eng J 17, 175–180.CrossRefGoogle Scholar
  11. 11.
    Stockmann C., Losen M., Dahlems U., Knocke C., Gellissen G., Büchs J. (2003) Effect of oxygen supply on passaging, stabilizing and screening of recombinant Hansenula polymorpha production strains in test tube cultures. FEMS Yeast Res 4, 195–205.PubMedCrossRefGoogle Scholar
  12. 12.
    Houston J.G., Banks M. (1997) The chemical-biological interface: developments in automated and miniaturised screening technology. Curr Opin Biotechnol 8, 734–740.PubMedCrossRefGoogle Scholar
  13. 13.
    Duetz W.A., Ruedi L., Hermann R., O’Connor K., Büchs J., Witholt B. (2000) Methods for intense aeration, growth, storage and replication of bacterial strains in microtiter plates. Appl Environ Microbiol 66, 2641–2646.PubMedCrossRefGoogle Scholar
  14. 14.
    Micro-24 MicroReactor System. See
  15. 15.
    Doig S.D., Diep A., Baganz F. (2005) Characterisation of a novel miniaturized bubble column bioreactor for high throughput cell cultivation. Biochem Eng J 23, 97–105.CrossRefGoogle Scholar
  16. 16.
    Betts J.I., Doig S.D., Baganz F. (2006) The characterization and application of a miniature 10 ml stirred-tank bioreactor, showing scale-down equivalence with a conventional 7L reactor. Biotechnol Prog 22, 681–688.PubMedCrossRefGoogle Scholar
  17. 17.
    Gilla N.K., Appletonb M., Baganza F., and Lye G.J. (2008) Design and characterisation of a miniature stirred bioreactor system for parallel microbial fermentations. Biochem Eng J 39, 164–176.CrossRefGoogle Scholar
  18. 18.
    Xie D., Shao Z., Achkar J., Zha W., Frost J.W., and Zhao H. (2006) Microbial synthesis of Triacetic Acid Lactone. Biotechnol Bioeng 93, 727–736.PubMedCrossRefGoogle Scholar
  19. 19.
    Funke M., Buchenauer A., Schnakenberg U., Mokwa W., Diederichs S., Mertens A., Muller C., Kensy F., Buchs J. (2010) Microfluidic BioLector—Microfluidic Bioprocess Control in Microtiter Plates. Biotechnol Bioeng 107, 497–505.PubMedCrossRefGoogle Scholar
  20. 20.
    Amanullah A., Otero J.M., Mikola M., Hsu A., Zhang J., Aunins J., Schreyer HB., Hope J.A., Russo A.P. (2010) Novel micro-bioreactor high throughput technology for cell culture process development: Reproducibility and scalability assessment of fed-batch CHO cultures. Biotechnol Bioeng 106, 57–67.PubMedGoogle Scholar
  21. 21.
    Cellstation high throughput bioreactors. See
  22. 22.
    DAS GIP parallel system for microbial fermentation in process development. See

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.DuPont Central Research and Development, Division of Biochemical Science and EngineeringWilmingtonUSA

Personalised recommendations