Microbial Physiology and Fermentation Technology course

Advanced Course

Microbial Physiology and Fermentation Technology

Course description

This very successful course will be held in 2023 for the 34th time! The course aims to familiarize participants with the integrated, interdisciplinary approach required in modern biotechnology. Microbial physiologists, metabolic engineers and (bio)process engineers from the faculty staff, together with invited (inter)national experts from other universities and industry, will offer a combination of lectures, exercises and demonstration experiments. In this way, the course will present an intensive and in-depth treatment of the state of the art. At the same time, the course provides the necessary link between, on one hand, fundamental subjects (e.g. stochiometry/kinetics of metabolic networks, physiology/systems biology) and, on the other hand, applications for design of microorganisms and and optimization of large-scale biotechnological processes.

17 – 26 January 2024

Delft University of Technology, the Netherlands

A limited number of fellowships is available for PhD students (reduced fee).

THE COURSE

Advanced Course Microbial Physiology and Fermentation Technology

For a better understanding of the lectures and to enhance active participation, this intensive two-weeks course consists of lectures, practical demo’s, computer simulations, exercises and case studies.

Morning and evening

course_Microbial-Physiology The lectures are mainly scheduled in the mornings and the early evenings. In the lectures, attention will be paid to the following themes:

Energy transduction and growth thermodynamics
Kinetics and stoichiometry of growth and product formation
Regulation of metabolism by environmental parameters
High-cell density fermentation
Metabolic networks: stoichiometry and fluxes
Rate based design
Regulation and control of metabolic fluxes
Metabolic engineering
Heterogeneity and mixed cultures
Capita selecta

Afternoon

Demo’s in fed-batch fermentation. Discussions and interpretation of results. On- and off-line measurements in the gas and liquid phase of reaction parameters and determination of the kinetics of biological conversions. Statistical data processing using mass balances. Tutorials in setting-up and simulating computer models of metabolic networks. Introduction to methods for upscaling. Possibilities to visit the research projects of the Biotechnology Department.

Study load

The course (including preparatory materials) is valued 98 hours of work.

Who should attend?

This Advanced Course is aimed at professionals (MSc, PhD or equivalent experience) in microbiology, biochemistry or biochemical engineering with a basic working knowledge of the two other disciplines. Also, molecular biologists with a microbial background may apply. The course is primarily aimed at those already employed in industry who wish to up-date their theoretical knowledge and practical insight in this field. In addition, this Advanced Course is an option in the two-year postgraduate programs of Delft University of Technology.

Course registration

Please register clicking the tab Register to attend the course. Applicants will be handled in order of the date of receipt.

PROGRAMME

Below the programme for 2024:

	Wednesday, 17-1-2024 Theme: Thermodynamics, balances and q-rates
08.30	Registration
08.45	Short introduction of how to use the Surface and course book
09.00	Outline of the course	Sef Heijnen
09.15	Basic energetics of microbial metabolism	Robbert Kleerebezem
10.30	Balances	Sef Heijnen
11.45	q-rates	Sef Heijnen
12.15	Lunch
13.15	Parallel sessions:
	Exercises on energetics of microbial metabolism Exercises on balances and q-rates	Sef Heijnen Robbert Kleerebezem
17.45	Social drink and buffet

	Thursday, 18-1-2024 Theme: Kinetics and stoichiometry of growth, product formation, process design and membranes transport
09.00	Black box model: kinetics / parametrization	Walter van Gulik
10.00	Black box model: stoichiometry	Walter van Gulik
11.15	Introduction to bioprocess design (batch, continuous)	Sef Heijnen
12.00	Exercises on bioprocess reactions in design	Sef Heijnen & Walter van Gulik
12.30	Lunch
13.30	Exercises on bioprocess reactions in design	Sef Heijnen & Walter van Gulik
15.45	Plenary discussion	Sef Heijnen & Walter van Gulik
16:15	Transport over biological membranes: mechanisms and thermodynamics	Walter van Gulik
17.25	End of the day

	Friday, 19-1-2024 Themes: Regulation of metabolism by environmental parameters, fed batch fermentation design and fermentation data analysis
09.00	Primary metabolism and its regulation	Pascale Daran – Lapujade
10.00	Microbial growth with mixtures of carbon substrates	Han de Winde
11.00	Physiological aspects of high cell density fermentation	Han de Winde
12.00	Lunch & group picture
13.00	Fed-batch fermentation and transport phenomena	Sef Heijnen
14.30	Exercises on data analysis of fermentation processes	Sef Heijnen & Robbert Kleerebezem
17.30	Optional: Lab techniques tour at the department of Biotechnology followed by a drink
17.30	Drinks

	Monday, 22-1-2024 Theme: Metabolic networks: stoichiometry, energy and application
09.00	Metabolic network analysis	Walter van Gulik
10.30	Exercises: Metabolic pathway stoichiometry	Sef Heijnen & Walter van Gulik
12.30	Lunch
14.30	Bioenergetics of microbial growth and the cost of adaptation Part I	Joost Teixeira de Mattos
15.45	Bioenergetics of microbial growth and the cost of adaptation Part II	Joost Teixeira de Mattos
16.45	Metabolic studies in the industrial contexts	Ralf Takors
18.00	Drinks and Buffet


	Tuesday, 23-1-2024 Theme: Metabolic networks: modelling, rapid sampling, regulation
09.00	Metabolic flux balancing: theory and applications	Wouter van Winden
10.15	Computer exercises on metabolic network analysis	Wouter van Winden
12.45	Lunch
13.45	Analysis of in vivo kinetics: rapid sampling and metabolite analysis	Matthias Reuß
15.15	Multi-scale modelling of process dynamics in large-scale bioreactors	Matthias Reuß
16.15	Multi-level regulation of metabolic fluxes, transcripts versus fluxes	Pascale Daran – Lapujade
17.00	Single cell studies of micro-organisms / Microfluidics	Sander Tans
18.05	Optional: Lab techniques tour department of Biotechnology

	Wednesday, 24-1-2024 Theme: Case study “Ethanol from syngas”
09.00	Rate based design of biosystems	Sef Heijnen
09.30	Case study: Ethanol from syngas	Henk Noorman & Amit Deshmukh
12.15	Presentation by each team	Henk Noorman & Amit Deshmukh
12.45	Lunch and optional visit fermentation lab	Dirk Geerts/Erik de Hulster
14.00	Continuation case study	Henk Noorman & Amit Deshmukh
16.30	Presentation by each team	Henk Noorman & Amit Deshmukh
17.15	Gas Fermentation: a path to low carbon fuel and chemical production with impact	Bjorn Heijstra
18.25	End of the day

	Thursday, 25-1-2024 Theme: Metabolic engineering: Strategies and applications
09.00	Metabolic engineering strategies for reducing costs	Sef Heijnen
10.30	Exercises on metabolic engineering strategies for reducing costs	Sef Heijnen
12.30	Lunch and optional visit fermentation lab
13.30	From System Biology to Metabolic Engineering and Industrial Process Development using Clostridium acetobutylicum as a Platform Strain	Philippe Soucaille
14.30	Monascus ruber as cell factory for lactic acid production at low pH	Ruud Weusthuis
15.45	Evolutionary and reverse engineering of S. cerevisiae	Jean-Marc Daran
16.45	Microbial community engineering for production of chemicals and bioenergy	Robbert Kleerebezem
18.15	Course dinner

	Friday, 26-1-2024 Capita Selecta: Single cells limits, scale up/down origin
09.00	Through Van Leeuwenhoek’s eyes	Lesley Robertson
10.00	Spatio-temporal single-cell analysis in picoliter reactors	Dietrich Kohlheyer
11.15	The limits to growth: the challenge to dissipate energy	Matthias Heinemann
12.15	Lunch
13.15	Transcription factor-based biosensors for strain development	Jan Marienhagen
14.15	Fermentation scale-up and scale-down	Stefan de Kok
15.15	The origin of cellular life	Christophe Danelon
16.00	Evaluation and certification	Henk Noorman
16.30	Farewell drinks

LOCATION

The course will be held at:

Faculty of Applied Sciences (building 58)
Department of Biotechnology
Delft University of Technology
Van der Maasweg 9
2629 HZ Delft
The Netherlands
P +31 (0)15 278 1922
F +31 (0)15 278 2355
E BiotechDelft@tudelft.nl

FEE

Deadline for registration is 27-12-2023

The course fee is:

Early Bird	€3650,-*
Regular Fee	€3900,-
PhD Students	€1825,-**

*To be eligible for the reduced early bird fee you need to register before 8-11-2023. If this date is exceeded, the regular fee applies.

**A limited number of fellowships is available for PhD students. To apply, please include a copy of your registration as a PhD student from your university.

The fee includes course materials, lunches and the buffets and the course dinners as indicated on the program. The fee does not cover other meals or lodging. Hotel accommodation can be arranged at your request.

The course fee is preferably paid by bank transfer. Payment by PayPal is possible. TU Delft employees can use their internal (project) code.

Preparatory texts will be sent one month before start of the course and after receipt of the course fee. The complete set of course books will be supplied at the start of the course.

In the event of your cancellation before 22-11-2023, a full refund will be granted. After this date, a 25% fee charge can be made.

Delay of payment past the final deadline as indicated on the invoice may result in cancellation of entry to the course. Re-entry is only possible in case of vacancies and the regular fee will be applied. Payment terms and deadlines will be indicated on the invoice and/or provided in an e-mail after registration, but the course fee should always be paid before the start of the course.

When the number of participants is too low to have a fruitful course, the Institute BioTech Delft will cancel the event no later than six weeks before the start of the course. The course fee will be reimbursed within three weeks after cancellation. In case a speaker will not be able to present his/her lecture, due to unforeseen circumstances, BioTech Delft will arrange an equivalent replacement.

BROCHURES

Brochure 2023

LECTURERS

Course board

Prof. Sef Heijnen

After his MSc studies in Chemical Engineering, Sef Heijnen worked at DSM (then: Gist Brocades) for 15 years and in this period he also completed his PhD thesis in bioprocess technology at Delft University of Technology. In 1988, he became full professor and group leader in Cell Systems Engineering within the Department of Biotechnology of Delft University of Technology. He has an impressive track record: he is (co-) author of over 400 scientific publications, has supervised 50 PhD students and is a member of the Royal Netherlands Academy of Arts and Sciences (KNAW). His research interests are (1) metabolic engineering and systems biology applied to industrial microbial processes using Saccharomyces cerevisiae, Penicillium chrysogenum and Escherichia coli, (2) metabolome measurement and 13C-tracer analysis in steady state and dynamic conditions, and (3) thermodynamic and kinetic modelling of metabolism and fermentation. Prof. Heijnen teaches a wide variety of courses, and was elected at TU Delft’s 2003 ‘Leermeester’ (best lecturer).

Dr. Pascale Daran-Lapujade

Pascale Daran-Lapujade is assistant professor at the TU Delft Department of Biotechnology in the Industrial Microbiology section. Her research investigates the physiology of the yeast Saccharomyces cerevisiae, to unravel the molecular mechanisms that drive its response to diverse environmental stimuli and to identify the evolutionary circumstances that have shaped their genomes. Although many of her research questions are inspired by industrial applications of yeasts, she also seeks to contribute to a deeper understanding of fundamental aspects of cellular physiology and metabolism, using S. cerevisiae as a model. In addition she is editor of the journal FEMS Yeast Research and member of the board of the Microbial Biotechnology section of the Dutch Society for Microbiology (KNVM).

Faculty staff

Dr. Walter van Gulik

Delft University of Technology, Cell Systems Engineering, Delft, the Netherlands

Dr. Robbert Kleerebezem

Delft University of Technology, Environmental Biotechnology, Delft, the Netherlands

Guest lecturers

Prof. Matthias Heinemann

University of Groningen, Molecular Systems Biology Group, Groningen, the Netherlands

Dr. Dietrich Kohlheyer

Institute of Bio- and Geosciences, IBG-1: Biotechnology, Microscale Bioengineering Group, Forschungszentrum Jülich GmbH, Jülich, Germany

Dr. Stefan de Kok

Stefan de Kok obtained his PhD from Delft University of Technology by studying “metabolic engineering of free-energy (ATP) conserving reactions in Saccharomyces cerevisiae”. Afterwards, he moved to Amyris Inc. in California, where he worked on high-throughput, automated strain engineering technologies. Dr. De Kok led a project to optimize ligase cycling reaction (LCR) as a method for rapid and reliable assembly of up to 20 DNA parts into DNA constructs up to 20 kb. In addition, he was involved in metabolic engineering of yeast strains for farnesene production. Currently, Dr. de Kok works as scientist and project leader at Zymergen Inc. in California, where he utilizes robotic strain engineering technologies to develop microbes producing novel molecules, and to improve the performance of microbes used in industrial fermentation.

Dr. Jan Marienhagen

Institute of Bio- and Geosciences, IBG-1: Biotechnology, Synthetic Cell Factories Group, Forschungszentrum Jülich GmbH, Jülich, Germany

Prof. Henk Noorman

Henk Noorman was trained as Chemical Engineer from Groningen University (NL). He obtained a PhD in Bioprocess Technology from Delft University of Technology (NL, 1991), on microbal systems modeling. He became a post-doc fellow in a Nordic research consortium, and co-ordinated a fermentation scale-up project among academic groups in Sweden, Denmark and Norway. He then joined Gist-brocades and DSM in Delft (NL) and worked on fermentation development and implementation projects, mainly in the area of antibiotics and bio-based products. He also has been project manager for innovation projects, and received the DSM R&D Award 2010. Henk Noorman is currently working as Corporate Scientist Bioprocess Technology in the DSM Biotechnology Center and involved in numerous projects in Industrial Biotechnology, Food Specialties, Anti-Infectives, and the Corporate Research Program. In addition he is honorary professor at Technical University Delft working on Bioprocess Design and Integration. Teaching activities include courses in Delft, Wageningen (NL), Brac (Croatia) and Shanghai (China).

Prof. Matthias Reuss

Institut für Bioverfahrenstechnik, University Stuttgart, Germany

Prof. Ralf Takors

Institut für Bioverfahrenstechnik, University of Stuttgart, Germany

Sander Tans

Kalvi Institute of NanoScience, Delft University of Technology

FOM-Institute for Atomic and MOlecular Physics (AMOLF), Amsterdam

Prof. Joost Teixeira de Mattos

Swammerdam Institute for Life Sciences, SILS, University of Amsterdam, the Netherlands.

Prof. Ruud Weusthuis

Associate Professor Microbial Biotechnology Bioprocess Engineering Wageningen University & Research

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Testimonials

Microbial Physiology and Fermentation Technology 2023

As a protein biochemist using batch fermentation to express integral membrane proteins, I have long been interested in the course offered by TU delft in Microbial physiology and fermentation technology. TU Delft being a nerve-centre for such process development initiatives, has a series of courses offered around the year. So, it was exciting to have received word that there was an opening on account of a cancellation. I jumped at the opportunity. I found the in-depth lectures on mass balances, q-rates, stoichiometry of growth and product formation to be a great primer to subsequent topics such as fed batch fermentation design, metabolic networks and data analysis of fermentation experiments. Case studies on industrial fermentation helped me go through the process of how rate-based design of biosystems are formulated for very complex systems. The culmination of the course touched on single cells, and the limits of scale up/down and the origins of life itself in a mesmerizing series of lectures led my industrial experts. The problem sets / exercised interspersed with the lectures aided by world renowned experts provided a collaborative environment which fostered discussion and exposure to multiple schools of thought. This was most rewarding as people from various backgrounds put their heads together in problem solving in creative ways. The atmosphere of the venue, food and the beautiful neighbourhood where the university is situated is treat for those visiting Holland from abroad as it was for me. I loved biking on the cobble stoned roads and exploring museums, churches, and local farmers markets to sample stroopwafels and homemade cheese on the weekends. I would highly recommend this course for anyone in the microbiology or fermentation fields who is interested in learning from the experts and further honing their skills in these cutting-edge methods. Samuel Jayakanthan Principal Scientist, Protein chemistry and engineering, Vandstrom, Inc

Microbial Physiology and Fermentation Technology 2023

As a PhD student interested in cell factory engineering, I took this course to improve my understanding of fermentation technology. This course is packed with valuable information and is taught by highly experienced lecturers from both academia and industry. An average understanding of fermentation technology helps a lot, which can be obtained from the preparatory text and videos. For me, the most exciting part about this course was to gain insight into the industrial side of biotechnology, which has given me new and useful perspectives to my PhD project. I highly recommend this course to anyone whose work is in some way related to fermentation. Christoffer Rode PhD student, DTU Biosustain

Microbial Physiology and Fermentation Technology 2022

The Advanced Course on Microbial Physiology and Fermentation Technology taught me that an interdisciplinary approach and learning from real industry cases is crucial when developing a successful fermentation process. Learnings from the course will enable me to collaborate better with people working with different fields (fermentation team, strain engineers, modelling team and DSP team). The course is very intense, but well-organized social activities enables to refresh the brain and get ready for the next day. Beata Lehka Postdoctoral Researcher at the Technical University of Denmark (DTU)

Advanced Course