Are you intrigued by the relationships between gut microbiome and human health? Do you have a passion for unraveling the mysteries of ecological interactions at a molecular level? We invite enthusiastic and dedicated candidates to join our cutting-edge research team as a PhD student to delve into the intriguing world of host-microbiome interactions. The position is supported by a recently awarded NWO-M2 grant.

If you enjoy working in an interdisciplinary research team and are eager to contribute to the understanding of host-microbe interactions, then the Microbiome Engineering Group, which is part of the Swammerdam Institute for Life Sciences in the Faculty of science at the University of Amsterdam, is the place to be. The research group investigates the molecular and physiological basis of bacterial adaptation in response to the changing host environment and the implication on human health.

What are you going to do?
In this interdisciplinary PhD project, you will investigate whether we can use the microbiome to digest synthesized vitamin B5-like compounds, which are currently already available as food supplements, into compounds that can enhance coenzyme A metabolism. We will investigate whether this could be beneficial for the patients with an abnormal coenzyme A synthesis, such as in case of inflammatory bowel disease (IBD).

Research Objectives:

Your journey as a PhD candidate will revolve around two pivotal objectives:

1. Bacterial metabolization: Here, you will study how the interaction between the human microbiome and supplementation of pantetheine causes alterations in the microbiome and metabolic conversions of pantetheine. To do so, in vitro fermentation experiments will be performed with isotopically (deuterium) labelled pantetheine using individual fecal inoculum of IBD patients and healthy matching controls. Alterations in the structure and function of the microbiomes will be investigated and labelled pantetheine conversion products will be analyzed.
2. Physiological Implications: You will investigate whether the microbiome, feature of the colonic tissue or both dictates the metabolic fate of the supplied pantetheine. For this, we will determine the uptake capacity of murine colonocytes to the supplied pantetheine. This will be studied in an intestinal organ culture system (which includes collection of all tissues that structurally form the colon) using healthy and inflamed murine colon tissue, as well as invertebrate models. Healthy colonic tissue will then be inoculated with IBD-microbiome supplemented with pantetheine.

During your PhD research, you will apply a variety of techniques, including (but not limited to) anaerobic bacterial isolation and culturing, whole genome sequencing, analytical chemistry for targeted (using HPLC) and untargeted (using LC-MS) metabolomics, creation of mutant bacterial strains, enzymatic activity, Gut organ culturing, bioassays to measure gut function, RNAseq.

Tasks and responsibilities:

• complete a PhD thesis within the official appointment duration of four years;
• perform anaerobic bacterial isolation and culturing;
• identify bacterial enzyme involved in pantetheine conversion and create mutant of the identified gene-encoding

enzymes;

• validate the effect of mutations on the physiology of the gut.
• ability to perform Bioinformatics and big data analysis, e.g. with Phyton, R or related program languages

(e.g. minor Programming or Bioinformatics);

• perform your experiments in a systematic and well controlled manner and keep accurate records by properly

documenting and organizing your work;

• be an active member of the research group and take responsibility for shared tasks.

Discuss your work with the group members and during consortium meetings. Incorporate feedback and

give input to others;

• take a leading role in writing manuscripts;
• participate in the Faculty of Science PhD training program;
• assist in teaching and supervise Bachelor and Master theses and tutoring students;

Ownership and Initiative: We are particularly interested in candidates who can take ownership of their research project and demonstrate initiative in driving their work forward. As a PhD student, you will have the opportunity to shape the direction of your research and contribute novel ideas to the field.

You will get the opportunity to:

• present your results at (inter)national scientific meetings;
• expand your academic, professional and personal skills;
• get access to cutting-edge facilities and technologies for innovative research;
• contribute to science communication and outreach efforts;
• thrive in a vibrant, impactful research community.

What do you have to offer?
You are passionate about science and have a particular interest in the human microbiome. You enjoy performing experimental lab work (e.g., molecular biology, analytical chemistry using HPLC and LC-MS, microbiology, molecular biology). You enjoy conducting data analyses through programming or other computational tools. You have a creative mind and look forward to work at the cutting-edge of technology. Finally, you are a team player and a pleasant colleague who enjoys being part of an interdisciplinary team of microbiology scientists.

A temporary contract for 38 hours per week, preferably starting on 1 June 2024, 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 € 2,770 in the first year to € 3,539 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.

Faculty of Science

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 29 March 2024. You can apply online by using the link below.

Applications in .pdf should include:

• a detailed CV including the months (not just years) when referring to your education and work experience;
• a letter of motivation;
• the names and email addresses of two references who can provide letters of recommendation.

The interviews will be held in the course of April 2024.

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