PhD Eco-evolutionary Dynamics in the Infant Microbiome

Microbial life occupies almost every habitat on Earth. There is increasing evidence that microbial communities living in and on plants and animals, including humans, play crucial roles, for instance in protecting their hosts against diseases. We are looking for an enthusiastic and highly motivated PhD candidate to study the eco-evolutionary processes that shape microbiomes in infants.

Are you curious about the interplay between microbiomes and human health outcomes and in how eco-evolutionary dynamics shape our microbiomes? Are you interested in bioinformatics and data analysis, and eager to apply and develop evolutionary and ecological theory? Then this may be the job for you!

You will be supervised by Dr. M. Bruijning, and embedded in the Evolutionary and Population Biology (EPB) department. EPB is part of the Institute for Biodiversity and Ecosystem Dynamics (IBED), the Faculty of Science at the University of Amsterdam. At EPB we work on the ecology and evolution of plants, animals and microorganisms in changing environments. We use different techniques ranging from laboratory experiments, theory, bioinformatics and molecular biology. You will collaborate with Computational Science Lab (CSL) in the Informatics Institute (IvI) to develop and deploy computational models. This position is supported by the NWA program (MetaHealth), focusing on oral and metabolic health in infants.

What are you going to do?
In humans, gut and oral microbiota develop rapidly during early life and are essential for our health during infancy and later in life. Many factors impact this development, including delivery modes and physical contact with family members, but also various ecological and evolutionary processes that act within the infants.

Recent genomic advances now enable strain-level characterization of the microbiome, paving the way for a deeper understanding of how host-associated microbial communities develop over time, ultimately aiming to predict efficient interventions to improve human health outcomes. Exciting questions include, for example, which microorganisms are transmitted from mothers to newborns, and do their strains persist during infant development? How do early life experiences impact the microbiome? Does within-infant microbiome evolution shape microbial communities, and does this vary with age and across body sites? Do Archaea, microbial symbionts parasitizing other microbes, and microbial viruses play a role in health and disease?

To address such questions, you will analyze data from the Amsterdam Infant Microbiome Study (AIMS) cohort, following infants and their families during the first 1000 days of their life. By analysing metagenomics data down to the strain level and integrating these observational data with theoretical, statistical and mechanistic models, you will test how microbiomes develop over time, and how this is shaped by ecological and evolutionary processes. You will develop skills in bioinformatics, statistics, multiscale modelling, community ecology and evolutionary biology.

Tasks and responsibilities:

• complete and defend a PhD thesis within the official appointment duration of four years
• closely collaborate with researchers within the MetaHealth consortium, including researchers that are collecting cohort and genomic data, and those using different computational and theoretical models
• get familiar with literature on human microbiome studies, and learn and apply bioinformatics (including (meta-) genomics, phylogenetics), statistics and theoretical modelling approaches
• discuss your work in our lab and group meetings, incorporate feedback and give input to others
• assist in teaching and supervising BSc/MSc students during their research internship
• participate in the Faculty of Science PhD training program
• present your work at (international) meetings

Your profile
You are an enthusiastic researcher who is excited about contributing new insights to the microbiome research and evolution field, and are interested in developing your theoretical, programming and statistics skills.

Your experience and profile

• interest in microbiome research and evolutionary biology
• completed (or nearly completed) MSc degree in the biological sciences or related fields
• a strong interest in data science, mathematics and/or modelling – including some proven experience in programming in e.g. R or python
• the willingness to learn new theoretical and computational methods
• good communication and collaboration skills
• experience in analyzing genomic data is welcomed

Our offer
The current position will be based in the Department of Evolutionary and Population Biology (EPB). Evolutionary and Population Biology Research in the department of Evolutionary and Population Biology focuses on understanding the ecological and evolutionary processes that drive community dynamics and speciation, and determine biodiversity patterns. At EPB, we are striving to offer a healthy working climate and an inclusive culture, where people with diverse backgrounds feel included and have the chance to bring and further develop their talents.

At EPB you will receive a temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). The preferred starting date is to be discussed. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.

The gross monthly salary, based on 38 hours per week and dependent on relevant experience, ranges between € 2,770 to € 3,539. This does not include 8% holiday allowance and 8,3% year-end allowance. The UFO profile PhD Candidate is applicable. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Universities of the Netherlands is applicable.

Besides the salary and a vibrant and inclusive environment at Science Park we offer you multiple fringe benefits:

• 232 holiday hours per year (based on fulltime) and extra holidays between Christmas and 1 January;
• multiple courses to follow from our Teaching and Learning Centre;
• a complete educational program for PhD students;
• multiple courses on topics such as leadership for academic staff;
• multiple courses on topics such as time management, handling stress and an online learning platform with 100+ different courses;
• 7 weeks birth leave (partner leave) with 100% salary;
• partly paid parental leave;
• the possibility to set up a workplace at home;
• a pension at ABP for which UvA pays two third part of the contribution;
• the possibility to follow courses to learn Dutch;
• help with registration at UvA- Housing for a studio or small apartment when you’re moving from abroad.

Are you curious to read more about our extensive package of secondary employment benefits, take a look here.

About us
The University of Amsterdam is the Netherlands' largest university, offering the widest range of academic programmes. At the UvA, 30,000 students, 6,000 staff members and 3,000 PhD candidates study and work in a diverse range of fields, connected by a culture of curiosity.

The Faculty of Science has a student body of around 8,000, as well as 1,800 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain.

Institute for Biodiversity and Ecosystem Dynamics

The Institute for Biodiversity and Ecosystem Dynamics (IBED) is one of eight research institutes of the Faculty of Science at the University of Amsterdam. The research at IBED aims to unravel how ecosystems function in all their complexity, and how they change due to natural processes and human activities. At its core lies an integrated systems approach to study biodiversity, ecosystems and the environment. IBED adopts this systems approach to ecosystems, addressing abiotic (soil and water quality) and biotic factors (ecology and evolution of plants, animals, and microorganisms), and the interplay between those. The IBED vision includes research encompassing experimental and theoretical approaches at a wide variety of temporal and spatial scales, i.e. from molecules and microorganisms to patterns and processes occurring at the global scale. The University of Amsterdam has excellent high performance computing facilities. Furthermore, IBED has a dedicated computational support team with specialized knowledge of bioinformatics, (geo)database management and scientific programming. IBED also works with non-academic partners to deliver transdisciplinary science for society.

Want to know more about our organisation? Read more about working at the University of Amsterdam.

Any questions?
Do you have any questions or do you require additional information? Please contact:

• Dr. Marjolein Bruijning: m.bruijning@uva.nl

Job application
If you feel the profile fits you, and you are interested in the job, we look forward to receiving your application. You can apply online via the button below. We accept applications until and including 1 September 2024.

Applications should include the following information (all files besides your cv should be submitted in one single pdf file):

• a detailed CV including the months (not just years) when referring to your education and work experience;
• a letter of motivation;
• the names and email addresses of two references who can provide letters of recommendation.

Only complete applications received within the response period via the link below will be considered. A knowledge security check can be part of the selection procedure (for details: National knowledge security guidelines). We will invite potential candidates for interviews soon after the closing date.

The UvA is an equal-opportunity employer. We prioritize diversity and are committed to creating an inclusive environment for everyone. We value a spirit of enquiry and perseverance, provide the space to keep asking questions, and promote a culture of curiosity and creativity.

No agencies please.

38 hours per week

Science Park 904