Skip to main content

This job has expired

PhD position in microbiota-pesticide-host interactions

Université de Lausanne
Switzerland (CH)
See link in description
Closing date
28 Feb 2024

View more

Bioinformatics, Ecology
Contract Type

Université de Lausanne (UNIL) is a leading international teaching and research institution, with over 5,000 employees and 17,000 students split between its Dorigny campus, CHUV and Epalinges. As an employer, UNIL encourages excellence, individual recognition and responsibility.

The Department of Fundamental Microbiology offers a PhD position in microbiota-pesticide-host interactions. The overall aim of this PhD will be to understand how the gut microbiota interacts with pesticides and how those interactions in turn affect the host.

Your responsibilities
The Engel lab ( utilizes social bees to address current questions about the evolution, ecology and functioning of gut microbiota-host interactions. We focus on social bees, specifically honey bees, because they harbor relatively simple, yet specialized gut microbes that are experimentally tractable. Moreover, bees are key pollinator across environments for both agriculture and natural ecosystem. Unfortunately, pollinator species are threatened by multiple environmental stressors, including pesticide exposure. While it has become clear that gut microbial communities can play a significant role in xenobiotic metabolism (e.g. drug metabolism in humans), the extent to which gut bacteria contribute to pesticide breakdown or toxicity in honey bees has remained elusive.

We have screened a large panel of pesticides for toxicity to and biotransformation by the bee gut microbiota. Your research will focus on understanding whether the most significant interactions in vitro induce corresponding results in vivo, and what effect this has on bee health and physiology.

Additionally, you will attempt to discover molecular mechanisms that underly resistance or biotransformation by microbes in the bee gut. As part of this effort, you will also investigate how long-term pesticide exposure may drive the evolution of pesticide resistance and what effect that has on susceptibility to other pesticides and antimicrobials. The research will be carried out in collaboration with a senior scientist in the lab, as well as with the group of Michael Zimmermann at the EMBL ( This collaborative effort will enable you to profit from the skills, facilities, and expertise of two of the leading molecular biology institutes in Europe.

Occasional travel to, or longer term stays at, EMBL Heidelberg may be included in your research activities.

At least 80% of the working time will be dedicated to personal research. The remainder may be dedicated to teaching (organization and supervision of student practicals).

Our group

Our group consists of both bioinformaticians and wet-lab biologists from all over the world, generously funded through the University of Lausanne and the Swiss National Science Foundation. We are part of the Department of Fundamental Microbiology, a highly collaborative, multidisciplinary, and team-oriented scientific environment with expertise in microbial ecology, evolution, molecular biology, cellular microbiology and biochemistry.

We are equipped with state-of-the art infrastructure enabling cutting-edge research with access to many core facilities located on campus (microscopy, proteomics, sequencing facilities). Our group has strong ties to other Departments within the University. Of particular importance for this project will be the collaboration with the lab of Michael Zimmermann at EMBL who are partners on this project jointly funded by the SNSF and the DFG.

We are also part of the NCCR Microbiomes, a national center for competence in microbiome research, which provides a collaborative research network including 23 groups in 6 institutions across Switzerland working on translational aspects of microbiome research.

Your qualifications

  • Applicants should have completed a Master’s thesis in molecular microbiology, microbial ecology, bioinformatics or a related field.
  • A strong understanding of microbiology and microbial metabolism is required.
  • Candidates with prior research experience in the fields of microbiome research, metabolomics, bioinformatics, molecular microbiology, insect physiology, or gnotobiotic animal experiments are highly desired.
  • A strong command of oral and written English is necessary for the lab environment.
  • We are looking for applicants who can demonstrate strong personal motivation to excel in science and curiosity in addressing highly relevant questions in microbiology, microbiome research, and bee health.
  • We offer a stimulating environment in a young international research group combining computational and experimental approaches to study microbial communities in the context of animal-microbe symbiosis and gut microbiota-host interactions.
  • The focus of the project can be adapted to the interests of the applicant.

What the position offers you
We offer a nice working place in a multicultural, diverse and dynamic academic environment. Opportunities for professional training, a lot of activities and other benefits to discover.

The city of Lausanne and its surroundings enable an excellent quality of life during your studies. Our department is situated on a beautiful campus on the shore of Lake Leman with a spectacular view of the Alps. Extensive and reliable public transport give you plenty of opportunities for outdoor activities by the lake and in the mountains. Lausanne is also centrally located within Europe, offering excellent train connections in all directions (Geneva airport: 1 hr; Zurich: 2 hr; Milan: 3.5 hr; Paris: 4 hr). 

UNIL is committed to equal opportunities and diversity.

UNIL supports early career researchers.

Additional information (Salary)
Doctoral student salaries are determined by the University and can be found in the following link:

Contact for further information
For questions concerning the application, position, or research topic, or in case of problems with accessing the UNIL career portal using the above link, please do not hesitate to contact Philipp at


Get job alerts

Create a job alert and receive personalised job recommendations straight to your inbox.

Create alert