PhD position in gut microbiota ecology and evolution

at  Universit de Lausanne

INTRODUCTION

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.

YOUR QUALIFICATIONS

MSc. PhD position applicants should have a Master thesis in microbiology, bioinformatics, ecology, or evolutionary biology. Prior research experience in large-scale sequence data analysis, microbial genomics and a keen interest for conceptual thinking in ecology and evolution would be desirable. A good command of the English language, a high personal motivation to excel in science and a curious mind are required.

We are looking for an outstanding and highly motivated candidate to join our research group to work on the gut microbiota of social bees. The thesis project will take place in the framework of the SNSF Consolidator grant project called ‘GLOBEE’ (https://engelbeelab.com/project/globee). In this project, we use computational and experimental approaches to study the ecology and evolution of the specialized gut microbiota across different social bee species. The project could include field work in Brazil and/or Malaysia (5%), high-throughput sequencing and bioinformatics analysis of metagenomics datasets (i.e. coding and using computing cluster, 70%), wet lab experiments if desired (5-20%) and writing and reading scientific literature (20%).This project will advance our general understanding of the evolution and ecology of gut microbiota across animals and elucidate the functional potential of the microbiota of key pollinators across a wide range of ecosystems.
Our group is part of the Department of Fundamental Microbiology, a highly collaborative, multidisciplinary, and team-oriented scientific environment. Our group consists of a diverse mix of microbiologists, ecologists and evolutionary biologists from all over the world that specialize in bioinformatics and wet-lab approaches, and are funded through the University of Lausanne and the Swiss National Science Foundation. We are equipped with state-of-the art infrastructures enabling cutting-edge research with access to many core facilities located on campus (microscopy, proteomics, sequencing facilities, computational cluster). We have strong ties to other Departments within the University, such as the Department of Ecology and Evolution, and also actively collaborate with other research teams within and outside of Switzerland, for example in Southeast Asia and Brazil. Last but not least, our department is situated on a beautiful campus at the shore of Lake Geneva with a great view of the Alps and with plenty of opportunities for outdoor activities.
In summary, the prospective PhD candidate will work on an exciting research project in a highly vibrant environment. Beside the possibility to publish impactful research papers, the student will be trained in cutting-edge bioinformatics analyses, obtain a deep understanding of microbial ecology and evolution, and acquire important skills in science communication and project management.
At least 80% of the working time will be dedicated to personal research. The remaining of the working time may be dedicated to teaching (organization and supervision of student practicals).
We expect the applicant to describe in their cover letter how their main interest matches the proposed PhD project and team and how they could tackle the proposed question.

For recent publications from the lab, please visit the lab webpage at https://engelbeelab.com/. Lab publications of particular relevance for this project includes (but are not limited to):

• Prasad, A., Pallujam, A. D., Siddaganga, R., Suryanarayanan, A., Mazel, F., Brockmann, A., … & Engel, P. (2024). Symbiont loss and gain, rather than co-diversification shapes honeybee gut microbiota diversity and function. bioRxiv, 2024-09.
• Sarton-Lohéac, G., Nunes da Silva, C. G., Mazel, F., Baud, G., de Bakker, V., Das, S., … & Engel, P. (2023). Deep divergence and genomic diversification of gut symbionts of neotropical stingless bees. MBio, 14(2), e03538-22.
• Ellegaard, K. M., Brochet, S., Bonilla‐Rosso, G., Emery, O., Glover, N., Hadadi, N., … & Engel, P. (2019). Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5. Molecular ecology, 28(9), 2224-2237.