PhD candidate Microbiome and Depression in Urban Mental Health

PhD candidate Microbiome and Depression in Urban Mental Health

Published Deadline Location
27 Nov 10 Jan Amsterdam

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Job description

The Swammerdam Institute for Life Sciences has a vacancy for a PhD candidate Microbiome and Depression in Urban Mental Health. 

Depression is the most prevalent psychiatric disease, mainly with an onset in adolescence and with a 30% higher prevalence in urban environments. Adolescence is arguably one of the most challenging and dynamic periods of development. Evidence from both preclinical and clinical research focusing on the established microbiota-gut-brain axis suggests that the etiology and pathophysiology of depression may be influenced by intestinal dysbiosis provocatively linked to urban risk factors. In fact, many if not all of the challenges faced by the developing adolescent in an urban environment have an impact on the intestinal commensal microbiota. Therefore, targeting the intestinal bacteria, and consequently the microbiota-gut-brain axis, to reduce adolescent depressive symptomatology is an innovative concept. The malleability of the nervous system at adolescence can be harnessed and may provide a critical window of opportunity. This goal asks for a three-tiered complexity approach, that analyses and integrates distinct levels of the gut brain axis

The Centre for Urban Mental Health research priority area has approved a PhD project at the University of Amsterdam between the faculty of Medicine (department of Psychiatry) and the Science faculty (Swammerdam Institute of Life Science). This project will be supervised by dr Anja Lok (psychiatrist) and prof. Stanley Brul (microbiologist / biochemist) and will be hosted at both faculties and the Institute for Advanced Studies of the University of Amsterdam. Therefore this project will be interdisciplinary by nature and you will work together with experts from various fields including methodology, psychology, psychiatry, biomedical and neurobiological science.

What are you going to do?

  1. Discovery phase: To investigate the impact of adolescent depression on individual and group microbial patterns over time. Microbiome will be assessed via 16 S rRNA sequencing data. Based on identified differences we will perform whole genome sequencing of selected differentially present microbes to probe for functional differences. The latter will indicate which physiological potential the metagenome has. Combined with the relative abundance and metabolomics measurements (already available in a large cohort, HELIUS study) the data will provide a basis for
  2. Mechanism exploration phase: using a biological systems approach we will analyze functional microbiota parameters in conjunction with the known host physiology i.e. depression;
  3. Proof of concept intervention phase: we will investigate the effectiveness of a microbial metabolite (butyrate) intervention on depressive symptoms and individual affective networks in adolescents as well as test effectiveness of additional identified microbial targets in proof of concept pre-clinical experiment.


University of Amsterdam (UvA)


What do we require?


  • have a completed research master, preferably in psychology (clinical, brain and cognition), biomedical science, medicine or a combination;
  • have a strong motivation for pursuing a PhD, also demonstrated with a high GPA during the master’s study;
  • have a Strong affinity with translational research: from model, to pre-clinical to clinical and therefore a multidisciplinary attitude;
  • have a strong affinity to (clinical) neurobiological research, system biology and especially the microbiome, and proficiency in statistics and programming in at least R;
  • have a good command of the English language, both spoken and written;
  • have a Special interest in the microbiome;
  • are socially skilled, being able to work in a laboratory but also with young psychiatric patients and have a multidisciplinary and collaborative mindset.

Conditions of employment

Fixed-term contract: four years.

A temporary contract for 38 hours per week, preferably starting asap, for a maximum period of four years (18 months plus a further 30 months after a positive performance evaluation) and should lead to a dissertation (PhD thesis). An educational plan will be drafted that includes attendance of courses and (international) meetings. Based on a full-time appointment (38 hours per week) the gross monthly salary will range from €2,325 in the first year to €2,972 in the final year, according to the Dutch salary scales for PhD candidates. This is excl. 8% holiday allowance and 8,3% end of year bonus. The Collective Labour Agreement of Dutch Universities is applicable.

Are you curious about our extensive package of secondary employment benefits? Then find out more about working at the Faculty of Science.


University of Amsterdam

With over 5,000 employees, 30,000 students and a budget of more than 600 million euros, the University of Amsterdam (UvA) is an intellectual hub within the Netherlands. Teaching and research at the UvA are conducted within seven faculties: Humanities, Social and Behavioural Sciences, Economics and Business, Law, Science, Medicine and Dentistry. Housed on four city campuses in or near the heart of Amsterdam, where disciplines come together and interact, the faculties have close links with thousands of researchers and hundreds of institutions at home and abroad.  

The UvA’s students and employees are independent thinkers, competent rebels who dare to question dogmas and aren’t satisfied with easy answers and standard solutions. To work at the UvA is to work in an independent, creative, innovative and international climate characterised by an open atmosphere and a genuine engagement with the city of Amsterdam and society.


Faculty of Science – Swammerdam Institute for Life Sciences

The Faculty of Science has a student body of around 6,500, 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.


  • PhD
  • Natural sciences
  • max. 38 hours per week
  • €2325—€2972 per month
  • University graduate
  • 19-809


University of Amsterdam (UvA)

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