The impact of the gut microbiome in human health is largely via its biocatalytic and biosynthesis capacity. In recent years, metagenomics-based approaches have identified various microbial species, even strains with specific genetic makeup, are involved in host’s immunity, metabolism, and drug response. However, detailed function of identified species remains to be experimentally confirmed. In LifeLines Microbiome Project, the information of disease, drug usage, genetics and the gut microbiome are available for over 8,000 individuals. Moreover, living gut microbes have been preserved. The aim of this project is to combine anaerobic culturomics with various biotechnological technologies and high-throughput omics profiling to functionally characterize bacterial species, and their genes that conduct biotransformation of various orally administered drugs. Specifically, the project includes:

1. Screening bacterial metabolism of commonly used drugs. Previous studies have shown that 66% of drugs can be consumed by gut species. By combining mass spectrometry analysis, it is possible to assess the mass differences before and after microbial transformation, thereby predicting underlying chemical transformation. In this project, we will co-culture bacterial isolates with drugs to investigate drug biotransformation by bacterial genes. In addition to single isolate analysis, we also test the drug metabolism capacity of microbial communities by culturing the whole gut microbial community. Moreover, we also assess the impact of drugs on microbial community and the cross-feeding relationship between bacteria.
2. Via genomic mining tools, bacterial structural variations and genes are identified to be related to host’s metabolism and immunity. In addition to isolate strains of interest from human samples, we will also apple molecular technologies to clone, mutate, delete the genes of interest for functional understanding.
3. Collaborate with colleagues from bioinformatics and organ-on-a-chip to understand host-microbe interaction in drug response and toxicity.

The PhD student working on these projects will be expected to:
- have an MSc degree in microbiology, biochemistry, pharmacy, or biomedicine;
- have experience in bacterial culture and metabolism are highly appreciated;
- be highly motivated and can work independently;
- have excellent communication skills in English, orally and writing;
- be a team player.

A fulltime (36 hours a week) PhD contract for 4 years and an excellent environment for further development. First, a temporary 1 year position will be offered with the option of renewal for another 3 years.

Your salary will be a minimum of € 2.631,- gross per month in the first year and a maximum of € 3.336,- gross per month (scale PhD per 1-8-2022) in the final (4th) year, based on a full-time appointment. 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).

Genetica

The UMCG is 1 of 5 medical research centers in the Netherlands. The student will be jointly supervised by Prof. Jingyuan Fu (Department of Genetics) and Dr. Hermie Harmsen (Department of Medical Microbiology and Infection prevention). We have an energetic, dynamic, and international working environment, with state-of-the-art laboratory and computing technology. The research team is very enthusiastic and has published several high impact papers on the gut microbiome. You can check the profiles of supervisors here:

Prof. Jingyuan Fu
https://scholar.google.nl/citations?user=7OHBkYMAAAAJ&hl=en
https://www.rug.nl/research/genetics/staff/jingyuan-fu

Associate Professor, Dr. Hermie Harmsen
https://www.rug.nl/staff/h.j.m.harmsen/?lang=en
https://scholar.google.com/citations?user=FRqPvk4AAAAJ&hl=en