The genome sequences of bacteriophages are among the most variable of all organisms. In this project, you will use phylome analysis to elucidate the evolutionary history of bacteriophages in the Crassvirales order and discover potential host links. Starting from a large collection of bacteriophage genomes that were extracted from metagenomic datasets, you will track the evolutionary events shaping these genomes, including horizontal transfer events, positive/negative selection, and host-specific mutations.

The research will be performed in two groups headed by Prof. Bas E. Dutilh: the Metagenomics Group (MGX) at Utrecht University (UU) and the Viral Ecology and Omics Group (VEO) at Friedrich Schiller University Jena (FSU). At UU, MGX is embedded in the Theoretical Biology and Bioinformatics Department and the Utrecht Bioinformatics Center. MGX studies genome evolution of uncultivated organisms, in particular viruses of microbes such as bacteriophages. At FSU, VEO is embedded in the Cluster of Excellence Balance of the Microverse and the Jena School for Microbial Communication. VEO studies the role of viruses in the functioning and dynamics of microbial communities.

Key publications:

• Dutilh et al. (2014), "A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes", Nature Communications 5: 4498.
• Edwards et al. (2016), "Computational approaches to predict bacteriophage-host relationships", FEMS Microbiology Reviews 40: 258.
• de Jonge et al. (2018) "Molecular and evolutionary determinants of bacteriophage host range", Trends in Microbiology 27: 51.

To excel in the role, we ask you to bring:

• a MSc in a relevant field involving bioinformatics;
• experience with comparative genomics techniques including genome annotation, evolutionary analysis, and phylogenetics;
• a strong interest in viruses;
• experience with Python, R, Snakemake/Nextflow, ETE Toolkit is beneficial;
• excellent communication skills (in English), ability to work as a team and to interact with people from diverse nationalities and scientific backgrounds in our cross-disciplinary scientific research groups.

We offer a position for 4 years divided between Utrecht University (NL) and Friedrich Schiller University Jena (DE). A unique opportunity to follow a PhD within two different institutions in two different countries. You will be embedded within a great team of world-class scientists who will support you on all aspects of the project.

The appointment starts at UU, during this period the terms and conditions of employment of UU apply: 

• A full-time gross salary ranging from € 2,541 to €3,247 in scale P;
• 8% holiday bonus and 8.3% end-of-year bonus;
• a pension scheme, partially paid parental leave, and flexible employment conditions based on the Collective Labour Agreement Dutch Universities.

In addition to the employment conditions laid down in the CAO for Dutch Universities, Utrecht University has a number of its own arrangements. For example, there are agreements on professional development, leave arrangements and sports. We also give you the opportunity to expand your terms of employment via the Employment Conditions Selection Model. This is how we like to encourage you to continue to grow. For more information, please visit working at the Faculty of Science. 

After approximately 22 months (depending on the starting date) you will be appointed at FSU according to the German employment conditions for PhD students. 

Utrecht University is a friendly and ambitious university at the heart of an ancient city. We love to welcome new scientists to our city – a thriving cultural hub that is consistently rated as one of the world’s happiest cities. We are renowned for our innovative interdisciplinary research and our emphasis on inspirational research and excellent education. We are equally well-known for our informal atmosphere and the can-do mentality of our people. This lively and inspiring academic environment attracts professors, researchers and PhD candidates from all over the globe, making both the University and the Faculty of Science a vibrant international and wonderfully diverse community.

At the Faculty of Science, there are 6 departments to make a fundamental connection with: Biology, Chemistry, Information and Computing Sciences, Mathematics, Pharmaceutical Sciences, and Physics. Each of these is made up of distinct institutes that work together to focus on answering some of humanity’s most pressing problems. More fundamental still are the individual research groups – the building blocks of our ambitious scientific projects. Find out more about working at the Faculty of Science.

Friedrich Schiller University is a traditional university with a strong research profile rooted in the heart of Germany. As a university covering all disciplines, it offers a wide range of subjects. Its research is focused on the areas Light—Life—Liberty. It is closely networked with non-research institutions, research companies and renowned cultural institutions. With around 18,000 students and more than 8,600 employees, the university plays a major role in shaping Jena’s character as a cosmopolitan and future-oriented city. Jena – City of Science: a young and lively town with a vibrant local cultural agenda. Jena is among the most liveable cities in Germany. Situated on the Saale River and surrounded by the famous Thuringian Forest, this city is ideal for lovers of nature and hiking. The university offers health promotion and a wide range of university sports activities.