Danmarks Tekniske Universitet

Multiple industries


PhD student in Strategies and tools to select E. coli fermenterphiles for industrial application at Danmarks Tekniske Universitet

The department (DTU-Biosustain) at the Technical University of Denmark invites applications for a position as a PhD student in Strategies and tools to select for industrial application.

This position will be placed at DTU-Biosustain, in the applied research group for High Density Physiology at the section of Translational Research, working with an aim towards bridging the gap between academic metabolic engineering projects from cell factories and their commercial application. We aim at establishment and integration of a whole workflow, from synthetic biology through genetic engineering, bench-scale fermentations and scale-up process design towards gate milestone driven project and process development until successful release into the market. The section has a total staff of approx. 30 employees, comprising of a highly motivated team of Engineers, Scientists and Technicians to tackle this challenging task. This project is happening in partnership with Dr. Gerd Seibold of DTU Bioengineering and Dr. Helena Junicke of DTU Chemical Engineering.

Responsibilities and tasks

Scale-up of bioprocesses rely heavily on selecting appropriate “”, i.e. robust production organisms that can show minor or no changes in the key process parameters at different cultivation scales. This PhD project aims to design and validate a strainbased on , a common production micro-organism for bio-based commodity chemicals (e.g. 1,4-BDO, 1,3-PDO, Succinic Acid). While is a well-studied microorganism, there exists a gap in understanding and engineering the production strain to be scale-independent, i.e. able to handle the inhomogeneous environment with chemical (pH, nutrient and dissolved oxygen) and physical (pressure, viscosity and temperature) gradients in a large-scale bioreactor.

Therefore, in this project, to engineer strains with scale-insensitive phenotype, you will

  • Develop suitable tools such as small-scale scale-down bioreactors to mimic the spatial heterogeneity of large-scale industrial bioreactors
  • Advance the knowledge of dynamic metabolic and transcriptional responses of in a large-scale fermentation using scale-down bioreactor models
  • Expand the adaptive laboratory evolutionary methods to adapt the strains to the constant changing conditions0
  • Derive a design to construct an improved and robust production strain


Candidates should have a Master's degree in engineering or a similar degree with an academic level equivalent to the Master's degree in engineering.

We are looking for a candidate with a solid background in

  • Bacterial metabolic network and metabolism
  • Quantitative microbial physiology
  • Bioprocess design principles and its application in bioprocess development
  • Bioreactor design and construction
  • Design and running of batch, fed-batch and continuous fermentations
  • Performing isotope labeled tracer experiments
  • Performing isotopically non-stationary 13C metabolic flux analysis (INST-MFA)
  • Strategies and methods to scale-up and scale-down of high-cell-density microbial fermentations
  • Rapid sampling and quenching methods to analyze intracellular metabolites
  • Analytical methods to measure intracellular metabolites using GCMS/LCMS
  • HPLC based analytical methods to measure metabolites
  • Methods to analyze RNA using Next Generation Sequencing techniques
  • Methods and experience in performing adaptive laboratory evolution
  • Data analysis and modelling software (Python, Copasi, Matlab etc…)
  • Black-box modelling, Stoichiometric modelling and Bioreactor modelling
  • Mathematical modelling, especially computational fluid dynamics
  • Project management
  • Scientific writing and communication in English

We expect that you are an efficient team worker, have good communication skills fluent in English, and have a critical approach to the formulation and testing of hypotheses. You are driven by a sustainable mindset and want to make a difference. Also, a good sense of humor will be appreciated.

Approval and Enrolment

The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programs at DTU. For information about our enrolment requirements and the general planning of the PhD study program, please see the DTU PhD Guide.

We offer

DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.


Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link "Apply online", fill out the online application form, and attach all your materials in English in one PDF file.

The file must include

  • A letter motivating the application (cover letter)
  • Curriculum Vitae
  • Grade transcripts and BSc/MSc diploma
  • Excel sheet with translation of grades to the Danish grading system (see guidelines and Excel spreadsheet here)

Remember to mention that you found this position on AU Job- og Projektbank