PhD Position in Gut Microbiome Dynamics and Environmental Interactions

PhD Position in Gut Microbiome Dynamics and Environmental Interactions

The Department of Genetics at the University Medical Center Groningen (UMCG) is seeking a highly motivated PhD candidate to work on microbiome dynamics in early life and its relationship with host and environmental factors in the birth cohort LLNEXT.

Closing date: July 1

Job description

This project is part of the Exposome-NL consortium, with a focus on evaluating how environmental exposures and host factors influence the microbiome development and overall health. The gut microbiome in about 4500 samples from over 700 LLNEXT participants is already profiled, and many other omics data layers (such as HMOs in human milk, vaginal microbiome, metabolomics and proteomics) are generated.

This PhD project will specifically focus on:

• Processing of newly generated longitudinal microbiome data in mothers and infants. This includes about 6000 samples for which metagenomic sequencing is currently being generated.
• Analysis of the development of gut and oral microbiome during pregnancy and in infants in relation to host and environmental factors.
• Functional analysis of microbial changes (including structural variations in bacterial genome) in relation to environmental factors.
• Integration of gut and oral microbes with multi-omics measurements such as metabolomics and immune profile, to understand the functional relevance of microbial changes during pregnancy and early life.

The candidate will work closely with members of the Groningen Microbiome Hub, an interdisciplinary group of over 25 researchers focusing on microbiome research in adult cohorts, mother–infant longitudinal studies, and clinical populations.

As a PhD candidate, you will:

• Integrate and analyze metagenomic, metabolomic, and environmental datasets.
• Design, develop, and maintain algorithms, tools, or infrastructure as needed.
• Present key findings in oral and written form at team meetings, international conferences, and through peer-reviewed publications.
• Collaborate within a multidisciplinary and international research team.

Working environment

You will join a dynamic and international department with strong expertise in bioinformatics, systems biology, and microbiome research. Our recent work has been published in top journals such as Science, Nature Genetics, Cell, and Gut.

• Nature 2022 (DOI: 10.1038/s41586-022-04567-7)
• Science 2016 (DOI: 10.1126/science.aad3369)
• Cell 2021 (DOI: 10.1016/j.cell.2021.03.024)
• Nature 2024 (DOI: 10.1038/s41586-023-06893-w)

Papers describing the LLNEXT cohort and microbiome studies in early life are:

• LLNEXT cohort description: E.Journal Epi, 2020: DOI: 10.1007/s10654-020-00614-7
• Gut microbiome development in pregnancy and early life (under revision): https://www.researchsquare.com/article/rs-5334252/v1
• Microbiome analysis in CS born babies: Cell Host and Microbe, 2024: DOI: 10.1016/j.chom.2024.07.010

The University of Groningen is ranked among the top 100 universities worldwide. The UMCG offers a stimulating training environment with opportunities to tailor your project to your interests and benefit from strong mentorship and collaboration.

What do we need

We are looking for candidates who have:

• An MSc degree in medical biology, mathematics, bioinformatics, computer science, or a related field.
• A strong motivation to conduct integrative biomedical research.
• Solid skills in mathematics, statistics, and/or computer science.
• Strong oral and written communication skills in English.

Bonus qualifications:

• Experience handling large-scale biological datasets.
• Programming experience (e.g., Java, Python, R).
• Background in biochemistry, metabolism, or systems biology.

What do we offer

• A fully funded 4-year PhD position. The initial contract is for one year, with an extension based on performance.
• A competitive monthly salary ranging from €3.017 (year 1) to €3.824 (year 4), based on full-time employment (scale PRO).
• Additional benefits include 8% holiday allowance and an 8.3% year-end bonus.
• Employment conditions follow the Collective Labour Agreement for University Medical Centres (CAO-UMC).
• Opportunities for training and career development.

More info:

• https://groningenmicrobiome.org/
• https://www.rug.nl/research/genetics/
• https://umcgresearch.org/w/lifelines-next

The University of Groningen is ranked among the top 100 universities worldwide. The UMCG offers a stimulating training environment with opportunities to tailor your project to your interests and benefit from strong mentorship and collaboration.