1 PhD Research position in Environmental and host effects on infant gut microbiome development in Belgium | KU Leuven

A position for a PhD student is vacant at the Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven in the laboratory of Prof. Jelle Matthijnssens under the umbrella of the Doctoral School Biomedical Sciences, Immunology and Microbiology.

Environmental and host effects on infant gut microbiome development

The Matthijnssens lab is a newly established lab focusing on the role of the human gut virome in human health and disease, using a recently optimized method to efficiently investigate viromes in fecal samples. The major lines of research are the role of the virome in Inflammatory Bowel Disease, the characterization of the developing human gut virome in infants, and the potential threat of bat viruses to human health. The Matthijnssens lab currently holds two PhD students and a post-doc.

The PhD project will be executed in close collaboration with Prof. Marc Van Ranst (Laboratory of clinical virology) and the Bioinformatics and (eco-) systems biology lab of Prof. Jeroen Raes, which are both part of the Rega Institute. Prof. Van Ranst and Prof. Raes will be the co-supervisor of the candidate. The KULeuven is ranked in the top-20 of best Universities in Europe, and the Rega Institute is worldwide renowned for its research on viral immunology and antiviral therapies.

The development of the intestinal microbiota is a key process in early life, as it significantly affects the metabolism and immune system of the host. Hence, the establishment of this symbiosis is of crucial importance to achieve and maintain optimal health. The human gut microbiota is a complex ecosystem of bacteria, viruses, fungi and parasites, influenced by external factors such as diet and the environment. The overall interplay between these different components of the microbiome as well as their dynamics over time are poorly understood. Furthermore, the microbiome is increasingly being implicated in several complex human diseases, despite the lack of baseline knowledge on the “healthy” microbiome at multiple-kingdom levels and its recruitment early in life.

The Ph.D. candidate will:

• study the development of the gut microbiome of infants during the first year of life, including bacteria, viruses, fungi and parasites using different metagenomics approaches (shotgun, 16S, 18S)
• perform state-of-the-art bioinformatics analyses, and develop/test different bioinformatics approaches to investigate trans-kingdom interactions in the developing human gut microbiome
• be responsible for the ongoing collection of stool samples from infants during the first year of life
• closely work together with other PhD and postdoctoral researchers on various microbiome research projects

Profile

• The candidate holds a Master of Science degree in Bioinformatics, Biomedical sciences, Bioengineering, Biochemistry, Biology and/or an adjacent field, or is expected to graduate before October 1st 2015
• The candidate should be graduated with at least one degree of distinction (>68%, KU Leuven eligibility criterion to start a PhD), although preference will be given to candidates with higher grades
• The ideal candidate has demonstrable experience with next-generation sequencing both in wet lab (BSL2) and dry lab environments. Knowledge of at least one scripting language (R, Python, Unix) is considered a strong plus. CThe candidate can work both independently as well as in an international team. Fluency in English is requiredandidates lacking wet lab experience are also encouraged to apply, but will be trained to work in the lab as well
• The candidate has strong analytical skills, an appropriate problem-solving attitude, can approach complex issues in a systematic way, is a good planner and able to meet deadlines

Offer

We offer you a full time PhD position for 4 years (with evaluation after the first year). Funding for the project is available. However, the candidate will be encouraged to apply for additional funding.