1887

A Simulator-Assisted Workshop for Teaching Chemostat Cultivation in Academic Classes on Microbial Physiology

    Authors: Xavier D. V. Hakkaart1, Jack T. Pronk1, Antonius J. A. van Maris1,2,*
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands; 2: Present address: Division of Industrial Biotechnology, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE 106 91, Stockholm, Sweden
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Received 23 December 2016 Accepted 05 August 2017 Published 04 October 2017
    • ©2017 Author(s). Published by the American Society for Microbiology
    • [open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/ and https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.

    • Supplemental materials available at http://asmscience.org/jmbe
    • *Corresponding author. Mailing address: Division of Industrial Biotechnology, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE 106 91, Stockholm, Sweden. E-mail: a.j.a.vanmaris@tudelft.nl.
    Source: J. Microbiol. Biol. Educ. October 2017 vol. 18 no. 3 doi:10.1128/jmbe.v18i3.1292
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    Abstract:

    Understanding microbial growth and metabolism is a key learning objective of microbiology and biotechnology courses, essential for understanding microbial ecology, microbial biotechnology and medical microbiology. Chemostat cultivation, a key research tool in microbial physiology that enables quantitative analysis of growth and metabolism under tightly defined conditions, provides a powerful platform to teach key features of microbial growth and metabolism.

    Substrate-limited chemostat cultivation can be mathematically described by four equations. These encompass mass balances for biomass and substrate, an empirical relation that describes distribution of consumed substrate over growth and maintenance energy requirements (Pirt equation), and a Monod-type equation that describes the relation between substrate concentration and substrate-consumption rate. The authors felt that the abstract nature of these mathematical equations and a lack of visualization contributed to a suboptimal operative understanding of quantitative microbial physiology among students who followed their Microbial Physiology B.Sc. courses.

    The studio-classroom workshop presented here was developed to improve student understanding of quantitative physiology by a set of question-guided simulations. Simulations are run on Chemostatus, a specially developed MATLAB-based program, which visualizes key parameters of simulated chemostat cultures as they proceed from dynamic growth conditions to steady state.

    In practice, the workshop stimulated active discussion between students and with their teachers. Moreover, its introduction coincided with increased average exam scores for questions on quantitative microbial physiology. The workshop can be easily implemented in formal microbial physiology courses or used by individuals seeking to test and improve their understanding of quantitative microbial physiology and/or chemostat cultivation.

Key Concept Ranking

Microbial Growth Kinetics
0.43121523
0.43121523

References & Citations

1. Bull AT2010The renaissance of continuous culture in the post-genomics ageJ Ind Microbiol Biotechnol37993102110.1007/s10295-010-0816-420835748 http://dx.doi.org/10.1007/s10295-010-0816-4
2. Monod J1949The growth of bacterial culturesAnnu Rev Microbiol337139410.1146/annurev.mi.03.100149.002103 http://dx.doi.org/10.1146/annurev.mi.03.100149.002103
3. Novick A, Szilard L1950Description of the chemostatScience112292071571610.1126/science.112.2920.71514787503 http://dx.doi.org/10.1126/science.112.2920.715
4. Herbert D, Elsworth R, Telling RC1956The continuous culture of bacteria; a theoretical and experimental studyJ Gen Microbiol1460162210.1099/00221287-14-3-60113346021 http://dx.doi.org/10.1099/00221287-14-3-601
5. Daran-Lapujade P, Daran JM, van Maris AJA, de Winde JH, Pronk JT2009Chemostat-based micro-array analysis in baker’s yeastAdv Microb Physiol5425731110.1016/S0065-2911(08)00004-0 http://dx.doi.org/10.1016/S0065-2911(08)00004-0
6. Monod J1950La technique de culture continue théorie et applicationsAnn Inst Pasteur (Paris)79390412
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8. Enfors SO2015Simuplot 4Available on www.enfors.eu
9. Pirt SJ1982Maintenance energy: a general model for energy-limited and energy-sufficient growthArch Microbiol13330030210.1007/BF005212947171288 http://dx.doi.org/10.1007/BF00521294
10. Pirt SJ1965The maintenance energy of bacteria in growing culturesProc R Soc London16322423110.1098/rspb.1965.0069 http://dx.doi.org/10.1098/rspb.1965.0069
11. Snoep JL, Mrwebi M, Schuurmans JM, Rohwer JM, Teixeira de Mattos MJ2009Control of specific growth rate in Saccharomyces cerevisiaeMicrobiology1551699170710.1099/mic.0.023119-019359324 http://dx.doi.org/10.1099/mic.0.023119-0
12. Diderich JA, Schepper M, van Hoek P, Luttik MAH, van Dijken JP, Pronk JT, Klaassen P, Boelens HFM, Teixeira de Mattos MJ, van Dam K, Kruckeberg AL1999Glucose uptake kinetics and transcription of HXT Genes in chemostat cultures of Saccharomyces cerevisiaeJ Biol Chem274153501535910.1074/jbc.274.22.1535010336421 http://dx.doi.org/10.1074/jbc.274.22.15350
13. van Uden N1967Transport-limited growth in the chemostat and its competitive inhibition; a theoretical treatmentArch Mikrobiol58214515410.1007/BF004066754878543 http://dx.doi.org/10.1007/BF00406675
14. de Jong-Gubbels P, Bauer J, Niederberger P, Stückrath I, van Dijken JP, Pronk JT1998Physiological characterisation of a pyruvate-carboxylase-negative Saccharomyces cerevisiae mutant in batch and chemostat culturesAntonie van Leeuwenhoek74425326310.1023/A:1001772613615 http://dx.doi.org/10.1023/A:1001772613615
15. Tagoe D, Ansah FK2010Computer keyboard and mice: potential sources of disease transmission and infectionsInt J Pub Health116
16. Harder W, Kuenen JG, Matin A1977Microbial selection in continuous cultureJ Appl Bacteriol4312410.1111/j.1365-2672.1977.tb00717.x332677 http://dx.doi.org/10.1111/j.1365-2672.1977.tb00717.x
17. Dijkhuizen DE, Hartl DL1983Selection in chemostatsMicrobiol Rev47150168
18. Novick A, Szilard L1950Experiments with the chemostat on spontaneous mutations in bacteriaProc Natl Acad Sci USA361270871910.1073/pnas.36.12.708148081601063276 http://dx.doi.org/10.1073/pnas.36.12.708
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2017-10-04
2017-12-17

Abstract:

Understanding microbial growth and metabolism is a key learning objective of microbiology and biotechnology courses, essential for understanding microbial ecology, microbial biotechnology and medical microbiology. Chemostat cultivation, a key research tool in microbial physiology that enables quantitative analysis of growth and metabolism under tightly defined conditions, provides a powerful platform to teach key features of microbial growth and metabolism.

Substrate-limited chemostat cultivation can be mathematically described by four equations. These encompass mass balances for biomass and substrate, an empirical relation that describes distribution of consumed substrate over growth and maintenance energy requirements (Pirt equation), and a Monod-type equation that describes the relation between substrate concentration and substrate-consumption rate. The authors felt that the abstract nature of these mathematical equations and a lack of visualization contributed to a suboptimal operative understanding of quantitative microbial physiology among students who followed their Microbial Physiology B.Sc. courses.

The studio-classroom workshop presented here was developed to improve student understanding of quantitative physiology by a set of question-guided simulations. Simulations are run on Chemostatus, a specially developed MATLAB-based program, which visualizes key parameters of simulated chemostat cultures as they proceed from dynamic growth conditions to steady state.

In practice, the workshop stimulated active discussion between students and with their teachers. Moreover, its introduction coincided with increased average exam scores for questions on quantitative microbial physiology. The workshop can be easily implemented in formal microbial physiology courses or used by individuals seeking to test and improve their understanding of quantitative microbial physiology and/or chemostat cultivation.

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Figures

Image of FIGURE 1

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FIGURE 1

Schematic representation of a chemostat set-up. F and F are volumetric flows, V represents the liquid volume and C represents a concentration. Subscripts in and out denote transport respectively into or from the reactor. Subscript s denotes the carbon and energy-source (substrate) and subscript x denotes biomass.

Source: J. Microbiol. Biol. Educ. October 2017 vol. 18 no. 3 doi:10.1128/jmbe.v18i3.1292
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Image of FIGURE 2

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FIGURE 2

Student performance on exam questions concerning continuous cultivations before (2014 and 2015) and after (2016) the introduction of the simulator workshop. A boxplot of the distribution of average grades of individual students on these questions for the regular exam (Panel A) and resit exams (Panel B) shows the minimum and maximum grades, the 25% and 75% quartiles (upper and lower limit of the box) and the median (black bar in the box). The asterisk indicates that the average grade was significantly higher in 2016 than in the two other years ( < 0.05 in a Student’s -test). Panel A: Student’s -test 2014 to 2016 < 0.001; 2015 to 2016 < 0.001. Panel B: Student’s -test 2014 to 2016 < 0.05; 2015 to 2016 < 0.001. The questions and the corresponding learning outcomes are provided in Appendix 5 . In the Dutch education system, students pass with a grade of 5.5 or higher. The percentage of students passing the exam questions that specifically dealt with steady-state chemostat conditions is shown for the regular exams (Panel C) and resit exams (Panel D).

Source: J. Microbiol. Biol. Educ. October 2017 vol. 18 no. 3 doi:10.1128/jmbe.v18i3.1292
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