PhD Candidate in Early-Life Gut Microbiome-Immune Interaction

University of Amsterdam; Netherlands; On-site; EUR 36,000 - 45,000; Full time

Benefits offered by this job

Holiday pay (8%)

End-of-year bonus (8.3%)

CAO NU applies

30% ruling may apply

Educational plan and courses

Teaching opportunities

Job summary

University of Amsterdam invites applications for a PhD position to study how the infant gut microbiome shapes immune development. Using the Gut-on-a-chip (GUMI), organoids, and omics, you will uncover microbial mediators of microbiota-immune interactions and contribute to interventions for better metabolic health.

You will work in an interdisciplinary team within SILS, with a four-year timeline and a starting preference of 1 January 2027, including teaching responsibilities and coursework.

Qualifications

• Hold, or be close to completing, an MSc in immunology, microbiology, molecular biology, biochemistry, biomedical sciences or a closely related field.
• Excellent written and spoken English communication.
• Ability to plan and conduct experimental work independently while collaborating with colleagues.

Responsibilities

• Complete a PhD thesis within the official appointment duration (four years).
• Design and conduct experiments on maternal factors, infant gut microbiota and intestinal health.
• Culture and characterize infant gut microbes using the GUMI platform and complementary methods.
• Use organoid and immune-competent gut-microbe co-culture models.
• Analyze omics and experimental data to identify key bacterial species, metabolites and genes.
• Communicate results through scientific publications and presentations within the project team.
• Contribute to teaching activities for Bachelor’s and Master’s students.

Skills

English communication

Independent experimentation

Interdisciplinary collaboration

Problem solving

Scientific writing

Education

MSc in immunology or related field

Job description

Help uncover how the infant gut microbiome shapes immune development

Do you want to investigate how the microbiome acquired in early life influences immune development and intestinal health? Join an ERC Starting Grant project that combines advanced gut-on-a-chip technology, organoid models and omics approaches. You will work in an interdisciplinary setting to identify microbial species, metabolites and genes that mediate microbiota‑immune interactions, generating knowledge that can support future interventions to improve metabolic health.

We welcome applications from candidates with diverse backgrounds, experiences and perspectives. If you recognise yourself in the role but do not meet every listed preference, we encourage you to apply.

This is what you will do

You will investigate interactions among maternal factors, the infant gut microbiota and intestinal health to uncover underlying mechanisms. Using the physiomimetic Gut-on-a-chip (GUMI) platform and omics analytical facilities, you will characterise metabolic functions of infant gut microbes under conditions relevant to clinical observations. You will use organoids and immune‑competent gut‑microbe co‑culture models to examine how early microbial colonisation affects immune‑cell development, gut epithelium and immunity, with particular attention to naïve T‑cell maturation.

Tasks and responsibilities:

• complete a PhD thesis within the official appointment duration (four years);
• designing and conducting experiments on maternal factors, infant gut microbiota and intestinal health;
• culturing and characterising infant gut microbes using the GUMI platform and complementary methods;
• using organoid and immune‑competent gut‑microbe co‑culture models;
• analysing omics and experimental data to identify key bacterial species, metabolites and genes;
• communicating results through scientific publications, presentations and collaboration within the project team;
• completing the PhD training programme of the Faculty of Science and contributing to teaching activities for Bachelor’s and Master’s students.

What we ask of you

You

• hold, or are close to completing, an MSc degree (or equivalent) in immunology, microbiology, molecular biology, biochemistry, biomedical sciences or a closely related field;
• communicate effectively in English, both in writing and in conversation;
• can plan and carry out experimental work independently while actively collaborating with colleagues in an interdisciplinary team;
• approach complex research questions with curiosity, careful problem solving and persistence;
• can document, analyse and communicate research results clearly and responsibly.

It is a preference if you have experience in one or more of the following: immune‑cell culture and profiling, flow cytometry, anaerobic bacterial cultivation, organoids, microphysiological systems, or omics data analysis.

This is what we offer you

We offer a temporary employment contract for 38 hours per week for a total duration of 4 years. The initial contract is for 18 months and, after satisfactory evaluation, will be extended to a total duration of 4 years. The preferred starting date is 1 January 2027. This appointment 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’s students.

Your salary will range between €3,204 in the first year to €4,051 gross per month in the last year of employment, based on a fulltime employment (38 hours per week). This sum does not include the 8% holiday pay and the 8.3% end‑of‑year bonus. A favorable tax agreement, the 30% ruling, may apply to non‑Dutch applicants. The Collective Labour Agreement for Dutch Universities (CAO NU) is applicable.

Are you curious to read more about our extensive package of secondary employment benefits, take a look here.

You will work in this team

The Faculty of Science has a student body of around 8,000, as well as 1,800 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, from elementary particles and the birth of the universe to the functioning of the brain.

You will work at the Swammerdam Institute for Life Sciences (SILS), one of the Faculty of Science’s largest institutes. Its approximately 240 scientists and staff members work in 19 research groups across four themes: Neurosciences, Cell & Systems Biology, Microbiology and Green Life Sciences. Within this project, you will contribute to ERC-funded research on early‑life microbiome and immune development. More information: https://sils.uva.nl/

The mission of the Molecular Biology and Microbial Food Safety group is to understand the interaction of microbes and their environment. We focus on microbiomes in the human gut and oral cavity in collaboration with our Amsterdam partners the Amsterdam UMC (location AMC) and ACTA. We study the gut microbiome in the context of Inflammatory Bowl disorders and the development of Depression whereas the oral microbiome is linked to Preventive Dentistry.

Want to know more about our organisation? Read more about working at the University of Amsterdam: https://www.uva.nl/en/about-the-uva/working-at-the-uva/working-at-the-uva.html

If you feel the profile fits you and you are interested in the position, we look forward to receiving your application. We accept applications until and including 13 October 2026.

If you have questions or require additional information, please contact:

• Dr Jianbo Zhang, [e-mail]