Assistant Professor in Microbiome Imaging and Functional Analysis
Assistant Professor in Microbiome Imaging and Functional Analysis
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€ 4 - 6
1 Vacancy
Job Description
Are you pioneering molecular tools and applying advanced imaging strategies to uncover how microbial communities are organized and interact in space and time If so we invite you to join The Swammerdam Institute for Life Sciences within the Faculty of Science at the University of Amsterdam.
Join us!
We are on the lookout for an enthusiastic and motivated scientist to enhance our research and educational the role of Assistant Professor in the Microbiome Engineering group which is embedded in the Microbiology theme you will have the chance to establish your own research agenda and contribute to teaching at both undergraduate and graduate levels.
One of our main research goals is to investigate how physical context shapes microbial behaviour from stress responses and gene regulation to metabolic activity and interspecies interactions. By integrating taxonomic identity with functional state and spatial positioning imaging-based methods provide a unique window into the organizational logic and resilience of microbial ecosystems.
The Microbiome Engineering group investigates how human gut microbes interact with their chemical and physical environment from nutrients and drugs to intestinal flow and motility. We combine microbial physiology and host modeling to uncover the ecological principles of hostmicrobe interactions focusing on spatial structure metabolic interdependence and functional adaptation of microbiota in health and disease.
As Assistant Professor you will contribute novel perspectives on microbial community organization and function using biotechnology advanced molecular labelling and spatial profiling approaches. Your work may address any ecological system from host-associated microbiomes to environmental microbial consortia where molecular aspects of spatial structure and community interactions are key. Your expertise will complement existing expertise in The Microbiome Engineering group and the broader Microbiology Theme and will allow strong collaborations with both experimental and big data-driven research groups within the Swammerdam Institute ranging from developmental biology to plant biology and neuroscience. Swammerdam Institute researchers also benefit from access to the Van Leeuwenhoek Centre for Advanced Microscopy (LCAM) which offers state-of-the-art imaging capabilities and collaborative addition various opportunities exist for collaboration at the University of Amsterdam outside the Swammerdam Institute e.g. within the Amsterdam Microbiome Expertise Centre and the nation-wide Holomicrobiome Institute.
What are you going to do
- investigate mechanisms and molecules involved in how spatial structure underpins microbial interactions adaptation and functional dynamics in complex environments;
- apply spatial imaging methods including but not limited to multiplexed FISH metabolic labelling barcoded probes or bio-orthogonal chemistry to study microbial organization and function in situ in complex microbial communities;
- collaborate with existing microbiome researchers bridge imaging data with molecular metabolic and physiological readouts;
- publish in peer-reviewed journals and present at international conferences;
- (co-)supervise PhD MSc and BSc student projects;
- participate in BSc and MSc teaching and curriculum development;
- actively seek external funding to support your research;
- participate in interdisciplinary collaborations across SILS and beyond.
What do you have to offer
You promote team science and create a safe working environment for a diverse community of researchers. Communication skills are important as well as a keen eye for innovations new developments and valorisation opportunities. You are a leader that connects and collaborates within the Institute the Faculty and the (inter-) national research community.
Your experience and profile
You have/are
- a PhD in microbiology synthetic biology biophysics or related fields;
- expertise in advanced molecular labeling and spatial profiling of microbial cells in situ including methods such as multiplexed FISH metabolic labeling spatial transcriptomics or combinatorial barcoding and their application to complex biological environments;
- experience or interest in (gut) microbial ecology and microbial physiology;
- a collaborative mindset and eagerness to bridge disciplines (e.g. with physicists chemists ecologists);
- willingness to contribute to valorization and outreach activities of the research group;
- experience with acquisition of funding;
- University Teaching Qualification (BKO) or the willingness to enrol in a program to achieve that within 2 years;
- fluent in spoken and written English. If you are not a native or fluent Dutch speaker you are expected to acquire sufficient proficiency in Dutch within three years of the start of your employment.
We will base our selection on your scientific track record and on your vision for future research and teaching teaching. We invite inspiring researchers who can push forward their original views and project ideas in the context of a highly competitive academic research environment to respond.
Our offer
We offer a temporary contract for 38 (1.0 FTE) hours a week preferably starting on 1 March 2026 for the duration of 18 months. A permanent contract follows after positive assessment of your performance. The job profile Assistant Professor 2 is applicable.
The salary depending on relevant experience before the beginning of the employment contract will be 4.728 6.433 gross per month. 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 for Dutch Universities). A favourable tax agreement the 30% ruling may apply to non-Dutch applicants.
Besides the salary and a vibrant and challenging environment at Science Park we offer you multiple fringe benefits:
- 232 holiday hours per year (based on fulltime employment);
- multiple courses to follow from our Teaching and Learning Centre;
- a pension at ABP for which UvA pays two third part of the contribution;
- the possibility to follow courses to learn Dutch;
- help with housing for a studio or small apartment when youre moving from abroad.
Are you curious to read more about our extensive package of secondary employment benefits take a look here.
Where you will work
The Swammerdam Institute for Life Sciences is located at the vibrant Amsterdam Science Park. SILS is one of eight institutes of the University of Amsterdams Faculty of Science (FNWI). With around 240 employees SILS carries out internationally high-quality life science research and provides education within various university programs. Research is also carried out in close cooperation with the medical biotech chemical flavor food & agricultural and high-tech industries and revolves around 4 main themes Cell & Systems biology Neurosciences Microbiology and Green Life Sciences
If this opportunity excites you and you meet the qualifications we look forward to your application! We accept applications until and including 1 October submit:
- a motivation letter and CV including a list of publications and your funding and teaching track record (if applicable);
- contact information for at least two academic referees;
- a 1-page research statement.
A knowledge security check can be part of the selection procedure(for details: National knowledge security guidelines).
For questions about the position or additional information please contact:
Employment Type
Full Time
