Novo Nordisk Foundation PhD scholarship in Multi-omic Analysis of Single Cell Protein Production from Methane

Thursday 08 Jul 21

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Biomanufacturing is one of the fastest growing fields and a driver for the transition from a fossil-based to a circular bio-based economy and a sustainable future. If you would like to become an expert in this strategically important interdisciplinary field and contribute to the green transition, we have an opportunity for you:

The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) at the Technical University of Denmark offers a position as a PhD student in multi-omic analysis of single cell protein production from methane. This position will be hosted at DTU Biosustain in the newly established C1 Metabolism group, headed by Prof. Lars Keld Nielsen and A/Prof Nikolaus Sonnenschein.

In order to realise emission reduction targets, we need to completely replace our current reliance on fossil fuels for the production of food, fibre and transportation fuel with a sustainable alternative. Plant biomass production is associated with its own challenges concerning water and land use and the disruption of the nitrogen and phosphate cycles with associated eutrophication. This challenge can be addressed by moving production to closed systems using photoautotrophic or chemoautotrophic microbes. This project is specifically focused on understanding single cell protein production with methanotrophs in the Unibio ( U-loop bioreactor process.

This PhD project is part of the PhD Program of the Fermentation Based Biomanufacturing (FBM) Initiative at DTU where we educate true biomanufacturing experts with interdisciplinary competences in cell factory-engineering and process engineering with a strong focus on industrial applications.

The FBM Initiative is funded by the Novo Nordisk Foundation, and under this initiative, scientists from DTU Chemical Engineering, DTU Bioengineering, and the Novo Nordisk Foundation Center for Biosustainability work together to engineer new or optimized production hosts or processes and solve the interdisciplinary challenges of large-scale bioproduction. The FBM Initiative’s research infrastructure includes a well-equipped fermentation core with an automation and high-throughput micro-fermentation unit, a pre-pilot plant and a pilot plant.

Located in the Copenhagen area, one of the world's strongest biotech hubs, DTU’s FBM Initiative offers a unique and internationally leading education and research environment with exceptional conditions for biotech career starters.

This is one of six PhD student positions available on the FBM PhD program this year.

The expected starting date is 1st of October 2021.

Responsibilities and qualifications
Natural gas fermentation in the U-loop bioreactor is a highly complex metabolic process with a co-culture of four different bacteria, including the main methanotrophic bacteria M. capsulatus. While significant understanding of the fermentation process in U-loop bioreactors has developed over the past years, there exists a knowledge gap in understanding the key metabolic shifts that occur in microbial metabolism during the fermentation. The primary focus of this PhD study is to create a baseline multi-omic understanding of the methane fermentation process in a pilot-scale (150L) U-loop bioreactor. This will contribute to a general understanding of M. capsulatus metabolism and its interaction with three other species as well as help to elucidate the metabolic bottlenecks faced by this microorganism at high productivity conditions in a U-loop bioreactor.

Specific tasks include:

  • Multi-omic data mapping of the SCP production process. You will sample Unibio’s pilot scale (150 L) bioreactor during startup and operation to quantitatively understand the metabolic and species-level interactions involved in the conversion of methane and nitrogen sources into biomass. Samples will be processed at DTU-Biosustain to extract proteome, exo-metabolome, endo-metabolome and fluxome of the co-culture process converting natural gas to single cell protein.
  • Genome reconstruction of 3 other species to illustrate the metabolic interaction in co-cultures. Using existing genome sequences, draft reconstructions will be generated through available model reconstruction pipelines. The resulting genome-scale reconstructions will be utilized to shed light on their functional importance in the co-culture and to facilitate subsequent data integration.
  • Computational data integration and thermodynamic analysis. In order to design better processes, the omics data will be integrated using the genome scale metabolic reconstruction to generate a dynamic flux balance model, incorporating simple models for substrate uptake as well as thermodynamically feasible flux distribution throughout the batch-fed batch and continuous start-up and operating phases.
  • Illustrate strategies for process intensification at pilot scale. Based on the model formulated above, strategies to overcome bottlenecks during start up as well as during process intensification will be developed and tested at pilot scale.

We are looking for a colleague with substantial knowledge of metabolic biochemistry, ideally with demonstrated experience in processing samples for omics analysis. You need to be comfortable working with computational modelling and ideally have prior experience with metabolic modelling including constraint-based and kinetic modelling.

Additionally, your CV will demonstrate ability to:

  • communicate technical information to internal/external audiences at various levels (undergraduates to senior scientists) and from various backgrounds (technical and non-technical personnel);
  • work independently and as part of a team; and
  • successfully work on multiple concurrent projects and meet deadlines.

You must have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.

Approval and Enrolment
The scholarships for the PhD degree are subject to academic approval, and the candidates will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, 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.

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 Professor Lars Keld Nielsen (, Associate Professor Nikolaus Sonnenschein ( or Senior Bioprocess Engineer Suresh Sudarsan (

You can read more about The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) at

If you are applying from abroad, you may find useful information on working in Denmark and at DTU at DTU – Moving to Denmark.

Application procedure
Your complete online application must be submitted no later than 30 July 2021 (Danish 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 – in the right hand column)

In the field “Please indicate which position(s) you would like to apply for”, please indicate which project you are applying for (title from the above list of PhD projects or individual research projects).

Incomplete applications will not be considered. You may apply prior to obtaining your master's degree but cannot begin before having received it.

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

The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain)
Recent progress in our ability to read and write genomic code, combined with advances in automation, analytics and data science, has fundamentally changed the scope and ambition of harnessing the potential of biological systems. Big data approaches and analysis of biological systems are key research instruments at the Center. DTU Biosustain utilizes these advances for microbial cell factory design to foster sustainable lifestyles in relation to three application areas: Sustainable Chemicals, Natural Products, and Microbial Foods. Learn more at

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 12,900 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. DTU has campuses in all parts of Denmark and in Greenland, and we collaborate with the best universities around the world.