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Early Stage Researcher (ESR4)  

PhD fellowship in Systems-level physiological characterization of Lactobacillus helveticus.

Project Title

“E-MUSE Complex microbial ecosystems multiscale modelling: mechanistic and data driven approaches integration” MSCA-ITN-2020 European Training Network

Hosting Organization

CHR. HANSEN A/S (CHRH), established in BOEGE ALLE 10-12, HOERSHOLM 2970, Denmark

Researcher Profiles


Research Field

Food microbiology, molecular microbiology, systems biology, microbial physiology, flavour formation, metabolic modeling

Application Deadline

31th May  2021, 23:59 - Europe/Brussels time

Envisaged Job Starting Date



4 years

Contract Type

full-time employment (based on COVID-19 evolution and restrictions, possibility to start remotely, once situation allows the presence is required)


The PhD project will focus on the in-depth physiological characterization of Lactobacillus helveticus, which is an industrially relevant bacterium commonly used in cheese ripening. The generated data will be integrated using state-of-the-art constraint-based modeling and data-driven approaches to gain system-level insights into the physiology and metabolism of the microorganism. The PhD position is an appointment which qualifies the candidate for further research positions within academia or industry and lasts for years. The majority of your working time will be devoted to the research project, but will also include course work, participation in project and group meetings as well as the dissemination of the research results through peer-reviewed publications and international conferences.

Expected Results

We expect to generate knowledge on the physiological characteristics of Lb. helveticus and the mechanisms underlying its contribution to cheese flavour and translate this knowledge into a genome-scale mechanistic model that is capable of simulating the organism’s phenotype under industrially relevant conditions. The experimental data generated in this project will also be provided to ESR1 for development and validation of computational methods and tools.

Your main tasks will include
•    Quantifying growth kinetics, sugar uptake and metabolite secretion in lab-scale bioreactors
•    Generating and analyzing various omics data, primarily metabolomics and transcriptomics, for achieving systems-level understanding of the physiology of Lactobacillus helveticus 
•    Mapping the biochemical basis and regulatory mechanisms underlying the organism’s contribution to flavor formation 
•    Simulating growth and flavor compound production under industrially relevant conditions through constraint-based modelling
•    Participating in the preparation of internal reports and scholarly articles for publications

Planned Secondments

In total, 2 months will be spent for modelling training and 4 months for integration of omics data into genome-scale metabolic models at the Vrije Universiteit Amsterdam in Netherlands.

Enrolment in Doctoral degree

Vrije Universiteit Amsterdam (VUA) (


Required Education Level

MSc degree in Systems Biology, Biochemical Engineering, Biotechnology or equivalent obtained no later than September 2021, combined with a research-oriented mindset

Skills / Qualifications


•    Good understanding of microbial physiology and metabolism
•    Hands-on experience with lab-scale fermentations
•    The ability to formulate a hypothesis and design appropriate experiments for its validation
•    Basic command of Python, Matlab and/or R.
•    Excellent oral and written communication skills in English
•    Ability to work in a dynamic, multicultural and interdisciplinary environment

•    Willingness to travel abroad for the purpose of research, training and dissemination

Specific Requirements

For the eligibility please check: Eligibility Criteria

Required Languages

English: B2, good oral and written communication skills in English are compulsory

Supervisors Team

Host Institution Description

The Systems Biology Unit at Chr. Hansen consists of three Departments, ‘SysBio Food’, ‘SysBio Health’ and ‘Bioinformatics & Modeling’, with a total of 26 employees. The 3 departments interact closely through the application of an integrative systems biology approach for decoding the molecular mechanisms underlying desirable microbial traits and generating comprehensive knowledge on Chr. Hansen’s strains. 

The Systems Biology Lab at Vrije Universiteit Amsterdam studies the molecular networks inside cells that give rise to cell behavior and fitness, in isolation and in interaction with other cells and their environment. The team focuses on the principles and general understanding of how those networks adapt in response to environmental and genetic changes and combine mathematical modelling, theory, and experiments. The approach is to apply the fundamental insights and methods in a biotechnological and biomedical setting.

The lead supervisor is Dr. A. Zeidan, currently heading the Systems Biology Unit at Chr. Hansen's R&D, which comprises 15 research scientists, 4 Industrial PhD students, 1 Industrial Postdoc, 4 research technicians and 2 Department Managers. Dr. Zeidan co-supervised 3 PhD students and more than 70 MSc students on their degree projects in the areas of microbiology, systems biology, biotechnology and food engineering.

The co-supervisor is prof. Dr. B. Teusink (VUA) – the head of the Systems Biology Lab, which he runs together with prof. Dr. F. Bruggeman at Vrije Universiteit Amsterdam. The focus is on understanding regulatory principles of microbial physiology and ecology.

Chr. Hansen is the world’s most sustainable food ingredients company and uniquely positioned to drive positive change through our microbial solutions, which touch the lives of more than 1 billion people every day.
Over more than 145 years, we have worked to enable sustainable agriculture, cleaner labels and healthier living for more people around the world. We have come far on our journey, and delivered strong results, and as we continue to unlock the power of good bacteria through new technologies, there is so much more we can do.
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.
Our employees are at the heart of everything we do and the driving force enabling us to live our mission to pioneer microbial science to improve food, health and productivity in our endeavor to grow a better world naturally.
Read more about working for Chr. Hansen at:

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