PhD scholarship in molecular microbial ecology; assessing the biosynthesis potential of ‘Microbial Dark Matter’ DTU Bioengineering Denmark

PhD scholarship in molecular microbial ecology; assessing the biosynthesis potential of ‘Microbial Dark Matter’

DTU Bioengineering

Apply no later than 19 February 2019

Apply for the job at DTU Bioengineering by completing the following form.


The Department of Biotechnology and Biomedicine (DTU Bioengineering) at the Technical University of Denmark invites highly motivated and talented candidates to apply for a fully funded three-year PhD scholarship within the areas of molecular microbial ecology and bioinformatics.


One of the greatest threats to human health is the rapid rise in antibiotic resistance in pathogenic bacteria and one of the main focus areas of the Molecular Microbial Ecology group is to counter this development by exploiting bioactive compounds produced by microorganisms. The advertised position is part of a high-profile ‘Sapere Aude’ project funded by the Independent Research Fund Denmark (DFF), aiming at obtaining novel antimicrobial compounds from the uncultivable majority of environmental microorganisms, i.e. ‘microbial dark matter’. 


Responsibilities and tasks

The main objective of the PhD project is to investigate the potential of natural microbial communities to produce novel bioactive compounds. Using high-throughput sequencing technology, the PhD student will assess and compare the biosynthesis potential of different microbiomes sampled across spatial scales and physico-chemical gradients. Ultimately, the data will provide a high-resolution map showing the most promising niches to mine for novel antimicrobial compounds. Furthermore, the student will be involved in the genome mining of hitherto uncultured bacteria from said niches and aid in the development of strategies for heterologous expression of biosynthetic gene clusters.


In this PhD project, the student will:

  • Identify and apply relevant methodology for the extraction of community DNA and collect corresponding metadata from various niches

  • Use high-throughput amplicon sequencing to investigate the potential for non-ribosomal peptide and polyketide biosynthesis in natural microbial communities

  • Couple the biosynthesis potential to relevant metadata (e.g. pH, salinity, species richness) using multivariate analyses

  • Sequence, assemble and mine bacterial genomes for the potential to produce novel antibiotics

  • Contribute to the development of cloning strategies for large gene clusters

The PhD project will be of a highly collaborative nature and draw on expertise from microbial ecologists, natural product chemists, metabolic engineers, and bioinformaticians from DTU Bioengineering, DTU Chemistry, DTU Biosustain, the Center for Microbial Secondary Metabolites (CeMiSt), as well as from international collaborators.


Candidates should have a two-year master's degree (120 ECTS points) or a similar degree with an academic level equivalent to a two-year master's degree.


We are looking for a candidate with a solid background in molecular microbial ecology who has an interest in analysing high-throughput sequencing data as the basis for understanding natural microbiological systems. The ideal candidate has experience with bioinformatics and the analysis of amplicon sequencing data as well as experience with modern molecular methodology in genetic engineering of bacteria.

Most importantly, we seek an ambitious candidate with a profound and intrinsic interest in science, who appreciates the challenges associated with such a project and has a positive and humorous nature.


Approval and Enrolment

The scholarship for the PhD degree is subject to academic approval, and the candidate will be enrolled in one of the general degree programmes at DTU. For information about our enrolment requirements and the general planning of the PhD study programme, please see the DTU PhD Guide.



The assessment of the applicants will be done by Assistant Professor Mikkel Bentzon-Tilia and Professor Lone Gram.


We offer
DTU is a leading technical university globally recognized for the excellence of its research, education, innovation and scientific advice. We offer a rewarding and challenging job in an international environment. We strive for academic excellence in an environment characterized by collegial respect and academic freedom tempered by responsibility.


Salary and appointment terms

The appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union. The period of employment is 3 years.


You can read more about career paths at DTU here.


Further information

Further information may be obtained from Assistant Professor Mikkel Bentzon-Tilia,


You can read more about DTU Bioengineering at www.bioengineering.dtu.dkand the project at



Please submit your online application no later than 19 February 2019 (local time).


To apply, please open the link "Apply online", fill out the online application form. The following must be attached in English:

  • A letter motivating the application (cover letter)

  • Curriculum vitae

  • Grade transcripts and BSc/MSc diploma

  • Excel sheet with translation of grades to the Danish grading system (see guidelines and Excel spreadsheet here)

Candidates may apply prior to obtaining their master's degree but cannot begin before having received it.


Applications and enclosures received after the deadline will not be considered.

All interested candidates irrespective of age, gender, race, disability, religion or ethnic background are encouraged to apply.


The Department of Biotechnology and Biomedicine (DTU Bioengineering) conducts research, educates future bio-engineers, provides scientific advice and innovate within the areas of microbiology, biochemistry, biotechnology and biomedicine. The research at DTU Bioengineering is at the highest international level and focuses on the societal and scientific challenges within the field. Research is conducted within three main areas: Microbial ecology and physiology, industrial biotechnology and cell factories, and Biomedicine and health. The department has extensive collaboration with national and international research units and industries. DTU Bioengineering has approx. 180 employees, of which 2/3 is scientific staff. The department is located at DTU, Lyngby Campus.


DTU is a technical university providing internationally leading research, education, innovation and scientific advice. Our staff of 6,000 advance science and technology to create innovative solutions that meet the demands of society, and our 11,200 students are being educated to address the technological challenges of the future. DTU is an independent academic university collaborating globally with business, industry, government and public agencies.

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