PhD Position in Computational Metabolic Modelling of the Infant Gut and Oral Microbiome

Gut and oral microbiota develop rapidly during early life and are essential for our health during infancy and later in life. Many factors potentially impact this development, including delivery modes, neonatal feeding (breast or formula), exposure to antibiotics, and maternal and infant diet. Changes in the microbiota by these factors can, in turn, substantially impact the immune system, hence the infant’s susceptibility to the development of chronic diseases. However, the mechanisms that relate these factors to our gut and oral microbiota are still unclear.

Understanding this complex interaction will pave the way to the discovery of new targets for interventions aimed at improving health. This position is supported by the NWA program METAHEALTH focusing on oral and metabolic health in infants.

You will be working in the Evolutionary Systems Biology team of dr. Meike Wortel. The team focusses on developing mathematical and computational techniques to include the environment, including other species, in the analysis of evolutionary trajectories and apply this to antibiotic resistance evolution and microbial communities. To achieve this, the team combines evolutionary approaches with systems biology, that links the intricate networks that make up cells to their overserved behavior at the cell level. The team is embedded in the Microbiology Cluster and affiliated with interdisciplinary collaborations in Systems Biology and research on Origin and Evolution of Life and Emergence. The team uses ongoing collaborations to link theory directly to experimental systems.

What are you going to do?
You are expected:

• to complete a PhD thesis within the official appointment duration of four years;
• to develop metabolic models of microbiome species and perform simulations in a community setting to study

the infant gut and oral microbiome and relate external factors, such as feeding behaviour, to changes

in the microbiota and the produced metabolites;

• to use published genome scale metabolic models, tune them with genomic information from cohort studies,

create new models, validate models with in vitro data, and develop methods for effective simulations

of communities;

• to closely collaborate with researchers within the METAHEALTH project performing in vitro experiments,

those analysing cohort data and those using different computational models. The aim is to produce

community models that represent the gut and oral microbiome for prediction of interventions that could

benefit infant health;

• to contribute to the teaching effort of the group, including supervision of bachelor and master students;
• to present your results at seminars and (inter)national conferences.

What do we require?

• a degree (MSc, or equivalent) in Systems Biology, Computational Biology, Mathematical Biology or

related fields. Candidates in the final stages of obtaining their degree are eligible to apply;

• fluency in English, both written and spoken;
• interest in studying biology with computational models;
• skilled in computational research, with strong programming skills;
• a strong interest for collaboration with experimental biologists;
• desirable methodological skills: experience with (genome scale) metabolic models;

knowledge of biochemistry and microbiology and good mathematical skills.

Our offer
We offer a temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.

Based on a full-time appointment (38 hours per week) the gross monthly salary will range from € 2770 in the first year to € 3539 (scale P) in the last year. This is exclusive 8% holiday allowance and 8.3% end-of-year bonus. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Dutch Universities is applicable.

Are you curious about our extensive package of secondary employment benefits like our excellent opportunities for study and development? Take a look here.

Questions?
Do you have questions about this vacancy? Or do you want to know more about our organisation? Please contact:

• dr. Meike Wortel
• Email: [email protected]

About us
The University of Amsterdam is the Netherlands' largest university, offering the widest range of academic programmes. At the UvA, 30,000 students, 6,000 staff members and 3,000 PhD candidates study and work in a diverse range of fields, connected by a culture of curiosity.

The Faculty of Science has a student body of around 7,000, as well as 1,600 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain.

The Swammerdam Institute for Life Sciences is one of the Faculty of Science’s largest institutes. Its approximately 240 scientists and staff members work in 19 research groups that perform excellent research centered on four themes: Neurosciences, Cell & Systems Biology, Microbiology and Green Life Sciences.

Want to know more about our organisation? Read more about working at the University of Amsterdam.

Application
Do you recognize yourself in the job profile? Then we look forward to receiving your application by 1 June 2024. You can apply online by using the link below.

Applications in .pdf should include:

• a motivation letter and CV, including a list of publications,
• contact information of referees.

Please mention the months (not just years) in your CV when referring to your education and work experience.

We will invite potential candidates for on-line and on-site interviews. The latter in the week starting with Monday June 10th or the week starting with Monday June 17th.

A knowledge security check can be part of the selection procedure.
(for details: National knowledge security guidelines)

The UvA is an equal-opportunity employer. We prioritize diversity and are committed to creating an inclusive environment for everyone. We value a spirit of enquiry and perseverance, provide the space to keep asking questions, and promote a culture of curiosity and creativity.

38 hours per week

Science Park 904