PhD student in the field of culturomics of the infant microbiome

PhD student in the field of culturomics of the infant microbiome

Published Deadline Location
12 Mar 21 Apr Groningen

Job description

The work of our group has characterized the colonization of the infant microbiome using several different data layers. These data layers include: (1) sequencing of the bacterial and viral microbiome throughout the infant’s first year of life; (2) characterization of the oligosaccharide content of breast milk, a potential ecological driver of selection for the infant’s microbiome; (3) and the metabolic profile of the infant’s blood plasma, which contains signatures of the interplay between host and microbiome. Important findings of these surveys indicate that particular species, such as Bifidobacterium spp. and Bacteroides spp., may serve as keystone species that promote the diversity and colonization of the microbiome. Other species, such as Staphylococcus spp., appear to be selected by oligosaccharides found in the mother’s milk. The aim of this PhD project is to study the role of such key species by culturing them from stool samples, characterizing their function via wet and dry lab approaches, and creating synthetic microbial communities from these isolates to test ecological and evolutionary theories of ecological succession and colonization. The focus of this project is therefore primarily lab based, although statistical and analytical experience is important to interpret results. Bioinformatic experience or an interest in learning the bioinformatic analyses is also a plus.

Information about our team and work:
Our team's website.

Links to recent papers from our team:
Paper: Environmental factors shaping the gut microbiome in a Dutch population
Paper: Host genetic regulation of human gut microbial structural variation

PhD student working on this project will be expected to:
- Perform microbiological analyses such as isolating and culturing isolates in both anaerobic and aerobic conditions.
- Perform molecular microbiology tasks such as DNA extraction and PCR.
- Set up and execute culture-based experiments.
- Process and analyze data from experiments.
- Summarize and report key analytical findings in both oral and written form at work meetings, at international scientific conferences and in scientific publications.


University Medical Centre Groningen (UMCG)


- An MSc in biology , microbiology, molecular biology or related field.
- Experience in a molecular or microbiological lab.
- Experience with statistics and performing analyses in R or python.
- Familiarity with ecological concepts.
- Excellent oral and written communication skills in English.

Bonus experience would be:
- Bioinformatic experience, such as genome assembly, annotation. Familiarity with shell scripting.

The UMCG has a preventive Hepatitis B policy. The UMCG can provide you with the vaccination, should it be required for your position.
In case of specific professions a ‘Certificate of Good Conduct’ is required.

Conditions of employment

You wil get a contract 32-36 hours a week for 4 years. Your salary will be a minimum of € 2.901,- gross per month in the first year and a maximum of € 3.677,- gross per month (scale PRO) 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).

Interested candidates should include a cover letter, CV, and references in their application.



We have an enthusiastic team and a strong bioinformatics group. Our microbiome studies were recently published in leading journals such as Science, Nature Genetics, Cell, and Gut. The Department of Genetics at the University Medical Center Groningen is an energetic, dynamic and international environment with state-of-the-art laboratory and computing technology.

Additional information

dr. Alexandra Zhernakova

dr. Cyrus Mallon


  • Research, development, innovation; PhD
  • Health
  • 32—36 hours per week
  • max. €2901 per month
  • University graduate
  • 240221


University Medical Centre Groningen (UMCG)

Learn more about this employer


Hanzeplein 1, 9713 GZ, Groningen

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Application procedure

dr. Alexandra Zhernakova,
dr. Cyrus Mallon,

Application procedure

Application procedure

dr. Alexandra Zhernakova,
dr. Cyrus Mallon,

Make sure to apply no later than 21 Apr 2024 23:59 (Europe/Amsterdam).