PhD project: Metabolic Modelling and Cultivation of Bacteria from Marine Sponges

Do you like bioinformatics and the laboratory? Would you then want to use your bio-informatics skills to reverse engineer cultivation conditions for currently uncultivable bacteria (which is the majority of bacteria in nature). Are you looking for a career in academia? We, the Laboratory of Microbiology of Wageningen University & Research (WUR) have an open PhD position for you!

We aim to use metabolic modelling to predict the primary metabolism of bacterial symbionts of marine sponges to get them to grow in vitro. Based on predictions of the secondary metabolism, these bacteria are a uniquely rich resource of bioactive molecules with pharmaceutical properties, but we can only proof and exploit this when they can be grown and for that reason we need you!

Our Aquatic Microbial Ecology group at the Laboratory of Microbiology is looking for a PhD student (4 years, full-time employment) as part of the European Union-funded research project XTREAM. The overarching goal of this research consortium of 13 universities, research institutes and companies is the sustainable exploration and biodiscovery of novel products and processes from extreme microbiomes with the aim to unlock their biological potential.

So what are you going to do?
As a PhD student you will work with one of the richest natural sources of newly discovered small molecules with bioactive properties. The current AI revolution offers whole new ways to isolate bacteria that are currently “biological dark matter”, i.e. uncultivable. For a bit more detailed outlook what the project entails, please see: “Improving the Odds: Artificial Intelligence and the Great Plate Count Anomaly”.

Your duties and responsibilities include:

• integrate omics knowledge of sponge-associated bacteria into genome-scale metabolic models;
• using (Fluorescence) Microscopy and Spatial Metabolomics to identify the location of target bacteria and metabolites in the sponge tissue;
• cultivation of the most wanted sponge-associated bacteria;
• collaborate with other researchers in the Aquatic Microbial Ecology group and the XTREAM consortium.

Requirements:

You have an MSc in the field of biology (i.e. biotechnology, microbiology, molecular biology) and experience with bioinformatics and with working in a laboratory (microbiology, cell culture, molecular biology). We are looking for a creative scientist who is eager to integrate AI to and wet lab microbiology, or in other words: someone who is not afraid of code and of getting dirty hands.

You also possess:

• affinity with cellular metabolism and/or biosynthetic pathways;
• experience with basic molecular biology laboratory techniques;
• a general interest in microbes;
• a collaborative attitude to work with other PhD students/postdocs from the XTREAM project and the Aquatic Microbial Ecology group.

In our international working environment there is an increasing amount of communication in English. For this position your command of the English language is expected to be at C1 level. Sometimes it is necessary to submit an internationally recognised Certificate of Proficiency in the English Language. More information can be found here.

You will work here:
Wageningen UR has a global reputation for its ground-breaking research and innovative education in the fields of environment, food and health - all of which make an essential contribution to the quality of life. Research at the Laboratory of Microbiology is characterized by a focus on innovative cultivation- and genomics-driven approaches, and applications in food, pharmaceutical and environmental biotechnology. The Aquatic Microbial Ecology group in the Laboratory of Microbiology is headed by Dr. Detmer Sipkema, who will be your main supervisor. We study interactions between marine eukaryotes (sponges, fish, algae) and bacteria just because we want to know how this works and linked to applications in pharma and food.

Salary Benefits:

Wageningen University & Research offers excellent terms of employment. A few highlights from our Collective Labour Agreement include:

• partially paid parental leave;
• working hours that can be discussed and arranged so that they allow for the best possible work-life balance;
• there is a strong focus on vitality and you can make use of the sports facilities available on campus for a small fee;
• a fixed December bonus of 8.3%;
• excellent pension scheme.

In addition to these first-rate employee benefits, you will receive a fully funded PhD position and you will be offered a course program tailored to your needs and the research team.

The gross salary for the first year is € 2.872,- per month rising to € 3.670,- in the fourth year in according to the Collective Labour Agreements for Dutch Universities (CAO-NU) (scale P). This is based on a full-time working week of 38 hours. We offer a temporary contract for 18 months which will be extended for the duration of the project if you perform well.

There are plenty of options for personal initiative in a learning environment, and we provide excellent training opportunities. We are offering a unique position in an international environment with a pleasant and open working atmosphere.

You are going to work at the greenest and most innovative campus in Holland, and at a university that has been chosen as the “Best University” in the Netherlands for the 19th consecutive time.

Coming from abroad
Wageningen University & Research is the university and research centre for life sciences. The themes we deal with are relevant to everyone around the world and Wageningen, therefore, has a large international community and a lot to offer to international employees.

Because we expect you to work and live in the Netherlands our team of advisors on Dutch immigration procedures will help you with the visa application procedures for yourself and, if applicable, for your family.
Feeling welcome also has everything to do with being well informed. We can assist you with any additional advice and information about for example helping your partner to find a job, housing, or schooling. Finally, certain categories of international staff may be eligible for a tax exemption on a part of their salary during the first five years in the Netherlands.

38 hours per week

Droevendaalsesteeg