PhD position - bioinformatica / microbioom

PhD position - bioinformatica / microbioom

Closing date: September 1

We are seeking a motivated and enthusiastic PhD student with a focus on computational biology, bioinformatics, and microbiome analysis to join a fully funded project on the role of the gut microbiome in cancer and cancer immunotherapy.

The Project

The project is funded by the Seerave Foundation and the candidate will become part of this international group of excellent scientists. The position will be in the department of gastroenterology and hepatology at the University Medical Center Groningen. The candidate will be embedded in the dynamic, productive and interdisciplinary Groningen Microbiome Hub which consists of several international groups studying different aspects of the human microbiome in various diseases and contexts. The University of Groningen is a top 100 University that has built a reputation for world-class research. You will follow courses and do research in small groups where personal interaction with your supervisor and other members of our team is an important part of your education.

Background
Treatment with Immune checkpoint blockade (ICB) has revolutionized oncology by prolonging survival of patients with different tumour types at the advanced stage, such as melanoma, non-small cell lung cancer, and renal cell carcinoma. However, only 30-50% of patients derive prolonged clinical benefit from ICBs, and some tumour types show limited response. In addition, ICBs distinct mode of activating the immune system causes unintended side-effects that are similar to autoimmune diseases, such as immune responses against normal tissues or organs. Evidence suggests that cancer patients’ gut microbiota differs from that of healthy individuals, and that the gut microbiota prior to ICB is associated with response, and immune-related adverse events. Part of the heterogeneity in response likely stems from the large strain-level variation within most bacterial species, with small genetic differences manifesting as considerable variation in phenotypes.

• Björk et al. 2024. Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma. Nature Medicine.
• Lee et al. 2022. Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. Nature Medicine.

Project aims

We aim to move beyond taxonomic annotation by pinpointing the bacterial strains and genes associated with response to cancer immunotherapy and side-effects using metagenomic sequencing and metabolomics data collected from several deeply phenotyped longitudinal observational cohorts and faecal microbiota transplantation (FMT) trials collected at the UMCG and with other Seerave collaborators. The PhD student will generate and work extensively with metagenome-assembled genomes (MAGs) and conduct, for example, pangenome and longitudinal strain-tracking analyses. The project combines state-of-the-art bioinformatics and statistical methodology with the overall goal of identifying bacterial strains likely responsible for eliciting anticancer immune responses that also minimize side-effects. There are also ample opportunities to be involved in other projects focusing on the role of the gut microbiome, diet and medication use in relation to cancer and cancer development within the group.

Required Expertise

• Master’s degree or equivalent, preferably with a focus on one of the following topics: Computational biology, Bioinformatics, Microbiome.
• Proficiency in R/Python, and command line.
• A collaborative spirit to work effectively within an interdisciplinary team.
• Excellent organizational and networking skills.
• Strong communication skills in English, both written and verbal.

What do we offer

This is a fixed-term appointment available for 3 years with a possibility for an extension for another year. The initial contract will be for one year followed by an extension, based on performance. The candidate will be provided with a stimulating work environment within the Groningen Microbiome Hub with opportunities for professional development within the field of microbial bioinformatics. Your salary will be a minimum of € 3.017,- gross per month in the first year and a maximum of € 3.824.- (from July on, a minimum of € 3.108,- and a maximum of € 3.939,-). In addition, the UMCG will offer you 8% holiday pay, and 8.3% end-of-year bonus. The conditions of employment comply with the Collective Labour Agreement for Medical Centres (CAO-UMC).

We are looking forward to the possibility of you joining our team to contribute to this groundbreaking research endeavor.

prof. Dr. Rinse Weersma gastroenterologist

dr. Johannes Björk Assistant professor