PhD scholarship in Impact of Streptomyces and their specialized metabolites on soil mock microbial communities

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The Technical University of Denmark

We are seeking a highly motivated PhD student to join our international team at the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain), Technical University of Denmark (DTU), and become part of the New Bioactive Compounds section and the Center for Microbial Secondary Metabolites (CeMiSt).


The New Bioactive Compounds section of DTU Biosustain aims at integrating advanced screening, computational biology and metabolic engineering in order to identify and characterize novel natural products, which could be candidates for antibiotics development.


We are members of CeMiSt, a Center of Excellence funded in 2018 by the Danish National Research Foundation. The Center is based at the Technical University of Denmark and hosted by the Department of Biotechnology and Biomedicine (DTU Bioengineering). Within the center, 10 senior faculty from DTU Bioengineering, DTU Chemistry and DTU Biosustain and >10 PhD students and postdocs aim to unravel the biological roles of microbial secondary metabolites in natural microbiological communities. The Center is led by Professor Lone Gram.


Within CeMiSt, a mock microbial community is being established originating from soil of one of our CeMiSt sampling sites in Denmark. From these soil samples, several streptomycetes were isolated that produce novel compounds. Your task will be to study the role of these Streptomyces secondary metabolites in soil microbial communities, by first identifying and characterize the biosynthetic pathways required for the biosynthesis of these compounds using our genome mining and CRISPR-based genome editing technology and then studying the effect of the engineered (knock-out) strains on the species diversity and functionality of soil mock-microbial communities.


Responsibilities and tasks

Tasks of this thesis project include:
  • You will take part in our genome mining efforts in order to identify the biosynthetic pathways of the identified novel natural products
  • You will use our CRISPR toolkit to inactivate biosynthetic genes and study their impact on the phenotype of the producer
  • You will test your strains in soil mock microbial communities that are developed in CeMiSt

You will work in close collaboration with the other scientists at DTU Biosustain, DTU Bioengineering and DTU Chemistry.


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 in biotechnology, microbiology, molecular biology or related field.

  • You have excellent laboratory skills and practical experience of state-of-the-art molecular microbiology methods and tools.
  • You have excellent knowledge of general microbiology and a good background in natural products biosynthesis and/or microbial ecology; knowledge and experimental experience in microbial natural products research, actinomycete biology or genetic / metabolic engineering are highly advantageous.
  • You have ambition, strong work ethics and attention to detail.
  • You have excellent communication and team-playing skills, but also the ability to work independently towards applied research goals in a multi-disciplinary international team of scientists.
  • You have excellent English skills for working in a highly international research group

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 candidates will be made by Professor Tilmann Weber and Associate Professor Ling Ding


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.

Expected start is spring/summer 2020.

You can read more about career paths at DTU here.

Further information

Further information may be obtained from Prof. Dr. Tilmann Weber, email: or Prof. Ling Ding (


Please do not send applications to this e-mail address; follow the electronic application and submission procedure as explained below.


Please provide contact details for two referees in your motivation letter or CV.


You can read more about DTU Biosustain at and about CeMiSt at


Please submit your online application no later than 25 February 2020 (23:59 local time).


Applications must be submitted as one PDF file containing all materials to be given consideration. To apply, please open the link “Apply online”, fill out the online application form, and attach all your materials in English in one PDF file. The file must include:

  • 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 Center for Microbial Secondary Metabolites aims to establish what effect microbial secondary metabolites have on other microorganisms in their natural environment. We have traditionally perceived them as ‘competition substances’, but in natural environments they are rarely produced in quantities of antibiotic effect. The Center’s hypothesis is that secondary metabolites constitute a network of signal molecules that directly affect gene expression, behaviour, and metabolism of the microorganisms and thus play a decisive role in the composition and function of microbiological communities. We will explore this in an interdisciplinary collaboration with the use of sequence-based, analytical-chemical, molecular, bioinformatic, and classic microbiological methods.


DTU Biosustain is an international research center of excellence developing next generation cell factories and bioprocesses for sustainable production of high-value chemical compounds. The center uses advanced metabolic engineering techniques and computational biology ensuring efficient and cost-effective design and construction processes.

The center’s activities are a balanced mix of basic and translational research, complemented by an emphasis on business development to facilitate commercialization of new cell factories and associated technologies. DTU Biosustain offers state-of-the-art research facilities and assembles world leaders in the field thus offering a unique platform providing excellent talent development and career opportunities.


Technology for people
DTU develops technology for people. With our international elite research and study programmes, we are helping to create a better world and to solve the global challenges formulated in the UN’s 17 Sustainable Development Goals. Hans Christian Ørsted founded DTU in 1829 with a clear vision to develop and create value using science and engineering to benefit society. That vision lives on today. DTU has 11,500 students and 6,000 employees. We work in an international atmosphere and have an inclusive, evolving, and informal working environment. Our main campus is in Kgs. Lyngby north of Copenhagen and we have campuses in Roskilde and Ballerup and in Sisimiut in Greenland.

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