PhD student in Strategies and tools to select E. coli fermenterphiles for industrial application

Monday 06 Jul 20

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The department Novo Nordisk Foundation Center for Biosustainability (DTU-Biosustain) at the Technical University of Denmark invites applications for a position as a PhD student in Strategies and tools to select E. coli fermenterphiles for industrial application.

The position is part of the FBM Initiative, which is funded by the Novo Nordisk Foundation.

The FBM Initiative is a collaboration between DTU Chemical Engineering, DTU Bioengineering, and the Novo Nordisk Foundation Center for Biosustainability. It offers research-based education in Fermentation Based Biomanufacturing for Master- and PhD- students, and professionals.
This position will be hosted at Novo Nordisk Foundation Center for Biosustainability and is one of seven PhD student positions available for the FBM PhD program this year.

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 “fermenterphiles”, 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 fermenterphile strain based on Escherichia coli, a common production micro-organism for bio-based commodity chemicals (e.g. 1,4-BDO, 1,3-PDO, Succinic Acid). While E. coli 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 E. coli 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 E. coli 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.

The assessment of the applicants will be made by Suresh Sudarsan and the collaborating scientists and approved by an internal PhD assessment committee.

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.

Salary and Appointment Terms
The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union. The period of employment is 3 years.

You can read more about career paths at DTU here.

Further information
Further information may be obtained from Suresh Sudarsan, or +45 93511777.

You can read more about DTU Biosustain at

Please submit your online application no later than 7 August 2020 (23:59 local time).

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

Candidates may apply prior to ob­tai­ning their Master's degree but cannot begin before having received it.

All interested candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.

The Fermentation Based Biomanufacturing (FBM) Initiative was founded as a response to the biotech industry’s increasing demand for specialized expertise in the fermentation area. Cutting-edge research, covering all aspects from fundamental physiology of production organisms/cell factories, synthetic biology and metabolic engineering, to scale-up process technology and downstream processing, provides the basis for the specialized FBM Education. The educational activities are developed in close dialogue with industry partners.

The FBM Initiative at DTU educates top-level candidates at MSc and PhD level, and provides research-based expertise for the biotechnological, chemical, and pharmaceutical fermentation based biomanufacturing industry.

The Department of DTU-Biosustain is located at DTU Lyngby campus. The center has established a world-class environment for research into the design and development of cell factories and new bio-industrial production methods. The goal is to further increase its socio-economic impact by developing microbial strains to significantly improve bio-sustainability. The center has approx. over 300 employees and aims to push the boundaries of existing knowledge in the field of biotechnology. Biotechnology will be a key element in the green transition, and thus, the center is a good example to promote sustainable products and processes in Denmark.

Technology for people
DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear vision to develop and create value using science and engineering to benefit society. That vision lives on today. DTU has 11,500 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. Our main campus is in Kgs. Lyngby north of Copenhagen and we have campuses in Roskilde and Ballerup and in Sisimiut in Greenland.