PhD Positions at the Forefront of Microbiome Research - METAMIC 3

PhD Positions at the Forefront of Microbiome Research - METAMIC 3

Join an exciting European research network at the forefront of microbiome science: two fully funded PhD positions in the Microbial Proteomics and Antimicrobial Resistance Groups at TU Delft (NL).     

Job description

About the research groups

Innovation is crucial to fulfil the potential of industrial biotechnology for sustainable production of fuels, chemicals, materials, food and feed. Similarly, scientific and technological advances in environmental biotechnology are needed to enable novel approaches to water purification, and ‘waste-to-product’ processes thus contributing to a circular economy. Increased fundamental knowledge encompassing enzymes, microorganisms and processes are essential for progress in this field. The Department of Biotechnology covers this research area and, based on new insights, selects, designs and tests new biobased catalysts, micro-organisms, and processes.

Within the Department of Biotechnology, the Microbial Proteomics and Antimicrobial Resistance research groups are joining forces to explore microbiomes in a One Health context using novel metaomics approaches, as part of the Marie Skłodowska-Curie Doctoral Network METAMIC. Martin Pabst’s group develops innovative microbial proteomics methods and data analysis pipelines to study the vast diversity of microbes and their communities, ranging from human-associated microbiomes to environmental systems involved in global biogeochemical cycles and engineered ecosystems for industrial use. Heike Schmitt’s group applies wastewater-based epidemiology (WBE) to monitor the circulation of WHO priority resistant pathogens in the general population and investigates how antimicrobial resistance (AMR) spreads from the environmental microbes to humans.

Job description

Two fully funded PhD positions (m/f/d) are available within the Microbial Proteomics and Antimicrobial Resistance research groups. The 2 PhD candidates perform their research within the framework of the Marie Skłodowska-Curie Doctoral network METAMIC 3 - Metaproteome-based leveraged microbiome management in the context of One Health. METAMIC is funded by the European Commission under the Horizon Europe framework programme (Grant Agreement number 101225682).

The METAMIC project will embed Doctoral Candidates (DCs) in a unique training environment to advance microbiome science through metaproteomics. The program addresses One Health challenges by integrating research on microbial mechanisms, microbiome dynamics in various ecosystems, and translational applications in clinical and biotech fields. DCs will benefit from expertise across molecular biology, bioinformatics, clinical research, and environmental science, supported by collaborations among academia, industry, and public sector partners.

Both PhD students will be part of a European training network and are expected to collaborate closely at TU Delft, but each will have a distinct project. One project will focus on advancing metaproteomics, including improving analysis throughput and quantitative techniques, using state-of-the-art equipment such as nano-flow systems and Orbitrap mass spectrometers. It will also involve developing and streamlining bioinformatics pipelines. The second project will apply metaproteomics and metagenomics to study hospital wastewater, focusing on antibiotic resistance genes in pathogens and the impact of antibiotics on microbial communities. Both PhD candidates will have the chance to conduct research visits at leading institutes, including the Leibniz Institute (Germany), University of Lille (France), and Erasmus Medical Center (Netherlands).

The goal is to screen hospital wastewater for antibiotic resistant pathogens using the metagenome and the metaproteome, with a focus on better understanding resistance mechanisms. Subsequently, we will determine the adverse influence of selected effectors (i.e. antibiotics) on the microbial wastewater communities in a series of experiments with differing complexity.

Job requirements

Your profile

• Masters, Diploma or equivalent degree in Chemistry, Bioinformatics, Biotechnology, Molecular Biology, Microbiology or similar
• Experience in fundamental biochemical and analytical methods, experiences with LC/MS, in particular proteomics or genomics are of advantage
• Proficiency in scientific English (written and spoken).
• Willingness to spend several months at other institutions abroad during secondments.
• Curiosity to perform fundamental and applied research.
• You are a great team player, and you like to work on a project within a large international consortium.

What we offer

• An exciting research topic combining fundamental research with applications, great training opportunities, and amble support for PhD students in framework of a collaborative training network;
• Working in an outstanding research institutes, collaborative, and with an international network;
• Training and scientific development opportunities and an excellent working atmosphere in a very dynamic and professional team;
• The opportunity to present your research at international conferences and participate in workshops.

TU Delft (Delft University of Technology)

Delft University of Technology is built on strong foundations. As creators of the world-famous Dutch waterworks and pioneers in biotech, TU Delft is a top international university combining science, engineering and design. It delivers world class results in education, research and innovation to address challenges in the areas of energy, climate, mobility, health and digital society. For generations, our engineers have proven to be entrepreneurial problem-solvers, both in business and in a social context.

At TU Delft we embrace diversity as one of our core values and we actively engage to be a university where you feel at home and can flourish. We value different perspectives and qualities. We believe this makes our work more innovative, the TU Delft community more vibrant and the world more just. Together, we imagine, invent and create solutions using technology to have a positive impact on a global scale. That is why we invite you to apply. Your application will receive fair consideration.

Challenge. Change. Impact!

Faculty Applied Sciences

With more than 1,100 employees, including 150 pioneering principal investigators, as well as a population of about 3,600 passionate students, the Faculty of Applied Sciences is an inspiring scientific ecosystem. Focusing on key enabling technologies, such as quantum- and nanotechnology, photonics, biotechnology, synthetic biology and materials for energy storage and conversion, our faculty aims to provide solutions to important problems of the 21st century. To that end, we educate innovative students in broad Bachelor's and specialist Master's programmes with a strong research component. Our scientists conduct ground-breaking fundamental and applied research in the fields of Life and Health Science & Technology, Nanoscience, Chemical Engineering, Radiation Science & Technology, and Engineering Physics. We are also training the next generation of high school teachers.

Conditions of employment

Doctoral candidates will be offered a 4-year period of employment in principle, but in the form of 2 employment contracts. An initial 1.5 year contract with an official go/no go progress assessment within 15 months. Followed by an additional contract for the remaining 2.5 years assuming everything goes well and performance requirements are met.

Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities, increasing from € 2901 per month in the first year to € 3707 in the fourth year. As a PhD candidate you will be enrolled in the TU Delft Graduate School. The TU Delft Graduate School provides an inspiring research environment with an excellent team of supervisors, academic staff and a mentor. The Doctoral Education Programme is aimed at developing your transferable, discipline-related and research skills.

The TU Delft offers a customisable compensation package, discounts on health insurance, and a monthly work costs contribution. Flexible work schedules can be arranged.

Successful candidates have to fully comply with the following essential eligibility criteria:

• Academic Qualification: The applicant must hold a relevant master’s degree or equivalent and must have obtained the degree or equivalent by the DC start date.
• In order to be recruited to the network as a doctoral candidate, applicants must not already be in possession of a doctoral degree (i.e. a Ph.D. degree).
• Conditions of international mobility of researchers: researchers must not have resided or carried out their main activity (work, studies, etc.) in the Netherlands for more than 12 months in the 3 years immediately prior to their recruitment.

Additional information

For more information about this vacancy, please contact Martin Pabst (m.pabst@tudelft.nl) or Heike Schmitt (h.schmitt@tudelft.nl).