项目介绍

2025年1月18日

The Laboratory of Viral Metagenomics (part of the Laboratory of Clinical and Epidemiological Virology) at the Rega Institute, headed by Prof. Jelle Matthijnssens, focuses on the role of the human gut virome in human health and disease. For virome analyses, we use the NetoVIR protocol to efficiently investigate viromes in fecal samples. The Matthijnssens lab currently houses eight PhD students and two lab technicians. Our group is now looking for a dynamic and highly motivated new student to join our research team and to start a 4-year PhD project under the umbrella of the Doctoral School Biomedical Sciences (https://gbiomed.kuleuven.be/english/phd).

The PhD project will be executed in close collaboration with Dr. Vanessa Harris (Department of Global Health, Amsterdam UMC, University of Amsterdam), Prof. George Armah (Noguchi Memorial Institute for Medical Research; NMIMR), and Michelo Simuyandi (Centre for Infectious Disease Research in Zambia; CIDRZ). These three collaborators are the research leads and partners of the ROTA-biotic study (Measuring the impact of rotavirus vaccines on pediatric antibiotics usage), funded by the Wellcome Trust (https://www.aighd.org/project/rota-biotic/).

KU Leuven is ranked in the top-20 of best universities in Europe, and the Rega Institute is world-renowned for its research on viral immunology and antiviral therapies.

Website van de eenheid

Project

This PhD project is embedded in the Afri-VIR project, which is funded by an FWO-grant (G041325N). The project will start in June 2025. The main goals of this project are as follows:

Infants are born with a nearly sterile gut, which is colonized rapidly after birth by bacteria, viruses, phages, and microbial eukaryotes derived from the mother or the environment. The infant enteric microbiota is essential to immune development, early-life metabolism, growth, and resistance to exogenous pathogens. This exact temporal process is still poorly understood, especially in low- and middle-income settings with high infant mortality. Although enteric viruses are often associated with disease, they are frequently asymptomatic and likely have underappreciated physiological roles. Viral-bacterial, viral-viral, and viral-host interactions have the potential to alter microbiome colonization and the training of host immunity.
In the Afri-VIR project, we will use longitudinal samples from infants in Ghana and Zambia to assess virome dynamics (1) in the first 100 days of life, when vaccines are administered and when children have the highest risk of infectious diseases and mortality, (2) across the first 500 days of life to assess longitudinal associations with environmental and sociodemographic variables, illness episodes, and antibiotic usage, and (3) we will screen phage genomes for the presence of antibiotic resistance genes to assess their role in the emergence of multi-drug resistant bacteria, contrasting our data with age-matched infants in distinct geographical and socio-economic settings (Belgium and Bangladesh) to identify common or distinct gut microbiome developmental patterns.
The PhD student will:

• Use wet lab viral metagenomics approaches to purify viruses and use Illumina (or related) NGS technology to investigate viruses and phages in longitudinal infant stool samples.
• Apply and optimize state-of-the-art bioinformatics analyses to investigate individual viruse and bacteriophages, as well as trans-kingdom interactions in the developing infant gut microbiome.
• Investigate longitudinal dynamics of the infant microbiota in relation to environmental factors such as diet, disease, treatment, and vaccination.
• Integrate the obtained phage data with available bacterial shotgun data for these samples.
• Compare obtained microbiota data with data from Belgian and Bangladeshi infants.

Profile

• You are passionate about scientific research!
• You hold a Master of Science degree in Biomedical sciences, Bioengineering, Bioinformatics, Biochemistry, Biology and/or an adjacent field, or are expected to graduate before October 1st 2019.
• You should have 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.
• Preferentially, you have experience with next-generation sequencing both in wet lab (BSL2) as well as in silico. Knowledge of scripting languages (R, Python,Unix) is considered a strong plus. Candidates lacking wet lab experience are also encouraged to apply, but will be trained to work in the lab as well.
• You can work both independently as well as in an international team. Fluency in English is required.
• You have strong analytical skills, an appropriate problem-solving attitude, you can approach complex issues in a systematic way, are a good planner and able to meet deadlines.

Offer

• A doctoral position for 4 years. Funding for the project is available. However, the candidate is expected to apply for additional funding.
• Work experience in a young, dynamic and internationally oriented research team.
• Many training opportunities and access to state-of-the-art technologies and infrastructure.
• Competitive salary and benefits package.
• Starting date: 1st of June 2025.

Interested?

Do you think you are the right person for this challenging PhD project?

Send us:

1) Your motivation letter, explaining why you are the perfect candidate for this position
2) Your Curriculum Vitae
3) Transcript of obtained grades
4) A list with at least two references (with name, function, email, address, phone number)

For more information please contact Prof. dr. Jelle Matthijnssens, tel.: +32 16 32 11 61, mail: jelle.matthijnssens@kuleuven.be or Mrs. Leen Beller, tel.: +32 16 32 12 85, mail: leen.beller@kuleuven.be.You can apply for this job no later than March 12, 2025 via the online application tool

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