Job description

Title: DC4, PhD fellowship in knowledge-driven design of plant-fermenting microbial cultures.
Researcher profile: Doctoral candidate.
Research field: Systems biology, Microbiology, Biotechnology, Biochemistry.
Type of contract: Temporary.
Job status: Full-time.
Duration: 36 months.
Application deadline: CLOSED.
Envisaged job starting date: October 2024.
How to apply: It is no longer possible to apply to this PhD position.

Hiring organisation and offer posting contact details

Organisation: Novonesis A/S.
Number of positions available: 1.
Country: Denmark.
Address: Gammel Venlighedsvej 14, 2970 Hørsholm.
Total duration of the stay at the recruiting organisation: 48 months.

Please note that this PhD position will lead to the award of a double diploma after the completion of a stay in each of these organisations: the Free University of Amsterdam (VUA), Netherlands and the University of Vigo (UVIGO), Spain.

Offer description

In brief:

We are looking for a Doctoral Candidate (DC) to join our project at multiple sites in the EU with a master’s degree in a relevant discipline (systems biology or a related field) interested in discovering microbial strains and cultures for fermentation of plant-based foods.

FAIROmics project:

The FAIROmics initiative, an interdisciplinary research programme, will gather universities, research centres and private companies to enable the FAIRification of omics data and databases interoperability and develop knowledge graphs for data-driven decision-making to rationally design microbial communities for imparting desirable characteristics to plant-based fermented foods in the context of open science and its regulations. The FAIROmics training programme aims to develop doctoral candidates’ skills at the interface between artificial intelligence, life sciences, humanities, and social sciences.

Scientific context:

Plant-based dairy and meat alternatives have grown in popularity in recent years for various reasons, including sustainability and health benefits, as well as lifestyle trends and dietary restrictions. However, plant-based food products can be nutritionally unbalanced, and their flavour profiles may limit their acceptance by consumers. Microorganisms have been used in making food products for millennia. However, the diversity of microbial communities driving plant-based fermentations, as well as their key genetic and phenotypic traits and potential synergies among community members, remain poorly characterised. Many data exist, but they are spread into different literature (scientific and grey) or, in the best case, in different databases. However, they are not always reusable because they are difficult to find and access and because databases are not systematically interoperable.

Objectives and expected results:

The aim of the PhD project is to identify strains and cultures that can improve the nutritional and/or organoleptic properties of plant-based materials through fermentation and gain a mechanistic understanding of the processes leading to such improvements. Using high-throughput screening, omics-level physiological characterization, statistical Design of Experiment and microbial community modelling, you will develop a workflow to rationally design microbial communities with the desired properties and obtain insights into the beneficial microbial interactions contributing to the community phenotype. 

Your main tasks will include:
- Designing and performing screening assays to identify strains that can ferment selected plant-based materials or impart beneficial product properties.
- Characterising strains at the phenotypic level by quantifying growth kinetics and metabolic activities in lab-scale bioreactors.
- Systematically assessing the community phenotype of strain combinations in co-culture fermentations.
- Generating and analysing various omics data for achieving a systems-level understanding of the strains' physiology and interactions between them.
- Designing microbial communities with synergistic properties by applying the generated data in combination with metabolic or statistical modelling.
- Participating in the preparation of internal reports and scientific articles for publication.

Planned secondments:

The secondment schedule will be as follows:
- Two secondments of three months each spent at the Free University of Amsterdam (VUA) on training in microfluidics-based investigation of microbial interactions and microbial community modelling.
- One secondment of six months spent at the Instituto de Investigacións Mariñas (IIM-CSIC) on ecological modelling and dynamic optimisation technologies.

Enrolment in Doctoral degree

1st-degree awarding organisation: Free University of Amsterdam (VUA), Netherlands, https://vu.nl/en
2nd-degree awarding organisation: University of Vigo (UVIGO), Spain, https://www.uvigo.gal/en

Required skills/qualifications

- Master's degree in systems biology, biotechnology, biochemistry, microbiology or a similar field.
- Good understanding of microbial physiology and metabolism.
- Knowledge of systems biology technologies such as transcriptomics, proteomics and metabolic modelling.
Experience with data analysis and programming in Python and/or R.
- Hands-on experience with microbial cultivations.
- The ability to formulate a hypothesis and design appropriate experiments for its validation.
- Ability to work in a dynamic, multicultural and interdisciplinary environment.
- Willingness to travel abroad for the purpose of research, training and dissemination.
- Excellent oral and written communication skills in English.

Eligibility criteria

- Any nationality
- Doctoral Candidate (DC): The applicant must not have been awarded a doctoral degree.
- Mobility rule: The DC must not have resided or carried out main activity (work, studies, etc.) in the country of their host organisation for more than 12 months* in the three years immediately prior to the date of selection in the same appointing international organisation.
* EXCLUDED: short stays such as holidays, compulsory national services such as mandatory military service and procedures for obtaining refugee status under the General Convention.
- Language: Applicants must demonstrate fluent reading, writing and speaking abilities in English (B2).

Supervisors team

The lead supervisor is Martin Holm Rau, Principal Scientist in the Bioinformatics and Modeling department at Novonesis. He has extensive expertise in the physiology of Lactic Acid Bacteria and in the systems biology characterisation of these. Most of his work aims at achieving a mechanistic understanding of bacterial phenotypes relevant to food fermentation, for example, by combining omics data analysis with metabolic modelling methods such as constraint-based modelling as well as data-driven methods such as machine learning.

The co-supervisor prof. Dr. B. Teusink (VUA) is the head of the Systems Bioinformatics group. Professor Teusink’s group currently houses 6 PhD students and two postdocs. Of previous students, 2 PhDs and 3 PDs now have a faculty position at Dutch Universities; 2 PhDs and 5 PDs moved to R&D jobs in industry; 3 PhDs are currently postdocs elsewhere, and 3 PhDs work as data analysts for bank and insurance companies.

The co-supervisor, Dr. Eva Balsa-Canto is leading the Biosystems and Bioprocess Engineering group (Bio2Eng). Her research areas include model identification and model-based optimisation and control of (bio)processes and biological systems. She has published around 100 papers, book chapters and congress proceedings, and has supervised 6 PhD students (plus three ongoing) and five postdocs. She has participated in and/or coordinated several national and EU-funded projects in (bio)process modelling and optimisation and systems biology. She will be involved in the training of modelling.

Host institutions description

In 2024 Chr. Hansen and Novozymes joined forces to form Novonesis.​ We are 10,000 people worldwide whose expertise spans more than 30 different industries. All around the world, our biosolutions already create value for thousands of customers and benefit the planet. Our biosolutions enable feeding and fueling the world more sustainably, from healthy and sustainable nutrition to biofuel. Our biosolutions also reduce the use of fossil-based resources, chemicals, energy and water. We are passionate about what we do because we know we can make a difference for people, animals and plants. And ultimately for our planet. It’s part of our culture, our history and our strategy. You will become a part of the Bioinformatics & Modeling team within the Microbe and Culture Research unit of Novonesis located in Hørsholm, Denmark, where most of your work will be carried out. We are an international team of nine computational researchers and one other PhD student, all collaborating closely with experimental scientists, with the aim of delivering biological insights for guiding the development of novel and innovative products.

The Systems Biology Lab houses both experimental and computational expertise. It is part of the Amsterdam Institute of Molecular and Life Science, offering expertise in relevant disciplines such as protein structure modelling and AI applications in biochemistry. The VU University offers bachelor and master teaching in the life sciences with a strong emphasis on the inter-disciplinarity of modern biology, with a strong focus on bioinformatics, systems biology, imaging, and multi-omics technologies in the priority areas of Health and Life Sciences and Science for Sustainability.

The Spanish National Research Council (CSIC) is the largest public research organisation in Spain and one of the most important in the European Research Area (ERA). It is the main player in the Spanish Science, Technology, and Innovation System and is currently made up of over 13,200 people. These individuals are distributed between the CSIC Corporate Organization, 121 research institutes, and three national centres located throughout Spain, as well as an institute in Rome. The CSIC conducts research in three core areas: Society, Life, and Material, which cover most academic disciplines. In March 2021, the CSIC was among the institutions awarded the 'HR Excellence in Research Award'.

We offer

- A comprehensive, interactive and international training programme covering the broader aspects and interface between life science, data science, artificial intelligence and humanities and social sciences, as well as transferable skills.
- An enthusiastic team of professionals to co-operate with.
- Personal Career Development Plan (PDCP) to prepare young researchers for their future careers.
- Each DC will undergo individual training at individual institutes according to the PCDP description.
- An attractive compensation package in accordance with the MSCA-DN programme regulations for doctoral candidates. The exact salary will be confirmed and will be based on a living allowance of 3400€/month (correction factor to be applied per country) + mobility allowance of 600€/month. Additionally, researchers may also qualify for a family allowance* of 660€/month, depending on the family situation. Taxation and social (including pension) contribution deductions based on national and company regulations will apply. 
*family = be married/be in a relationship with equivalent status to a marriage recognised by the legislation of the country or region where it was formalised/have dependent children who are being maintained by the researcher.

Selection process

1. Candidates apply for a position using the application form on the Novonesis website.
2. The DC supervisors will select the best candidates based on applications. At Novonesis, we commit to an inclusive recruitment process and equality of opportunity for all our job applicants. We recommend you not to attach a cover letter to your application. Instead, please include a few sentences about why you are applying in your resume/CV. Also, please attach your transcripts from undergraduate and postgraduate (if applicable) studies.
3. The selected applicants will be interviewed through an online meeting by the Selection Committee (two main supervisors and two representatives of a beneficiary or associated partner, with at least one person external to the DC’s project).
4. The best candidates will be chosen by the main supervisors.

To ensure a fair recruitment process, please refrain from adding a photo to your resume/CV. Novonesis is committed to creating a diverse environment and is proud to be an equal-opportunity and affirmative-action employer. All employment decisions are based on business needs without regard to race, skin color, ethnicity, religion, gender, gender identity or expression, sexual orientation, national origin, genetics, age, disability, or veteran status. 

Contact details: For questions about the position, please reach out to Kristian Jensen, Head of Bioinformatics and modeling at krje@novonesis.com  

Want to learn more?
Learn more about Novonesis, our purpose, and your career opportunities at novonesis.com

Not the right fit for you?
Even if this job isn't the right fit for you, perhaps you know someone who might find it interesting. If so, please feel free to share the job link and encourage them to apply. Thank you for your referral! Please check out our other open positions. The right fit for you could just be a few clicks away.