Dr Birgitta Ebert

Research Fellow in Synthetic Biolog

Australian Institute for Bioengineering and Nanotechnology
birgitta.ebert@uq.edu.au
+61 7 334 63179

Overview

Birgitta Ebert studied Chemical Engineering from 2000 to 2005 at the TU Dortmund University (Dortmund, Germany) with a specialization in biotechnology and technical chemistry. In her diploma thesis at the Chair of Chemical Biotechnology (TU Dortmund, Germany) she computationally analyzed and experimentally verified the metabolic potential of Escherichia coli for whole-cell redox biocatalysis.

During her PhD thesis, supervised by Prof. Dr. Andreas Schmid at the Chair of Chemical Biotechnology (TU Dortmund, Germany), she further applied systems biotechnological approaches to understand and engineer superior whole-cell redox biocatalysts.

From September 2011 to April 2019, Birgitta led a research group at the Institute of Applied Microbiology at RWTH Aachen University (Germany) focused on the rational engineering of microbes for the production of industrially relevant chemicals.

In April 2019, Birgitta joined the Vickers Group at the Australian Institute for Bioengineering and Nanotechnology at the University of Queensland. Her research interest centers on gaining a systems-level understanding of microbial metabolism and the application of this knowledge to engineer microorganisms into cell factories for natural products.

Research Interests

  • Systems Metabolic Engineering
  • Synthetic Biology

Qualifications

  • Doctor of Philosophy, TU Dortmund University

Publications

View all Publications

Grants

View all Grants

Supervision

  • Doctor Philosophy

  • Doctor Philosophy

View all Supervision

Available Projects

  • This project is embedded in a larger project on plastic waste valorization. In a hybrid approach, we thermo-chemically convert mixed plastic waste into small molecules, which are fed to bacteria for upcycling into biodegradable bioplastic.

    We work with Pseudomonas putida, a soil bacterium capable to grow on a broad variety of carbon sources including most molecules derived from plastic degradation. Your task will be to optimize the microbe for the simultaneous conversion of the substrate mix and the production of polyhydroxyalkanoates. Your tasks include the design of optimal metabolic pathway, the implementation of these designs in vivo via synthetic biology tools, characterization of the engineered strains for substrate conversion and product formation at shake-flask and bioreactor scale. In parallel to the targeted approaches, you will also perform adaptive laboratory evolution experiments to improve the fitness of the microbial strain towards toxic components contained in the plastic waste streams. Sequencing of evolved strains will allow us to identify key mutations, which we will reverse engineer into Pseudomonas.

    You will gain in-depth knowledge on the metabolism of Pseudomonas and practical skills in metabolic engineering and synthetic biology including, molecular biology, omics analyses, microbiological work, fermentation, and analytics.

    Honours and (under)graduate students are welcomed to work on specific subprojects.

    Please contact me for further information.

  • Modern protein-based vaccines require adjuvants to improve immunogenicity and hence efficacy. The natural product class of triterpenoids includes molecules that have been shown to be very potent vaccine adjuvants. From these candidates, squalene and Quillaja saponins have been approved for their use in vaccines against flu, shingles and malaria. And many more triterpenoid-adjuvanted vaccines are in the pipeline.

    These molecules are currently sourced from animal and plant-derived sources. Squalene is found in high abundance in the liver oil from (deep-sea) sharks and currently the only approved source for medical applications. The Quillaja saponins contained in QS-21 adjuvants are only produced by specific trees in limited regions in South America. Both species, sharks and Quillaja saponaria, are threatened by overexploitation. With the increasing demand for potent vaccines, this is expected to increase.

    In this project, we are working on the biotechnological production of these compounds with engineered Baker's yeast Saccharomyces cerevisiae. We can produce squalene and QS-21 precursors at the gram-scale level, which is the current state of the art.

    Within this larger project, two HDR projects are available focusing on (a) improving squalene production and secretion of the intracellular storage molecule into the fermentation medium, and (b) implementing the complex QS-21 biosynthesis pathways in the yeast chassis.

    Honours and (under)graduate students are welcomed to work on specific subprojects.

    You will gain in-depth knowledge on the metabolism of S. cerevisiae and practical skills in metabolic engineering and synthetic biology including, molecular biology, omics analyses, microbiological work, fermentation, and analytics.

    Please contact me for further information.

  • The yeast Saccharomyces cerevisiae is widely used in fermentation to produce wine, beer, and bioethanol. However, this well-researched microbe can also be efficiently engineered for the production of complex natural products. Well-known examples are the anti-malaria drug artemisinin are the ant-cancer drug paclitaxel.

    In this project, we are interested in the production of triterpenoids, the largest group in the natural product class. Many of these molecules have biological activities that make them promising candidates for pharma, nutraceutical, or cosme(ceu)tical applications.

    We have engineered a superior S. cerevisiae platform strain capable of the synthesis of diverse triterpenoids at the gram-scale level. In this project, we aim to expand the product spectrum to alpha-amyrin type triterpenoids with anti-ageing and anti-obesity properties that are used are investigated for use in cosmetics and pharmaceuticals.

    You will recombinantly express plant enzymes in the yeast chassis to enable the production of a few target products. You will further address a major bottleneck in the production of triterpenoids, the intracellular accumulation of the products, which results in cell toxification and low production efficiency. We are following alternative and complementary approaches including the expression of recently identified transporter, in situ extraction and optimization of the intracellular product trafficking route.

    You will gain in-depth knowledge on the metabolism of S. cerevisiae and practical skills in metabolic engineering and synthetic biology including, molecular biology, omics analyses, microscopy, fermentation, and analytics.

    Honours and (under)graduate students are welcomed to work on specific subprojects.

    Please contact me for further information.

View all Available Projects

Publications

Book Chapter

Journal Article

Conference Publication

  • Lehnen, M., Ebert, B. E. and Blank, L. M. (2016). Development of mini-bioreactors for evolution of thermotolerance. 11th Metabolic Engineering Conference 2016, Awaji Island, Japan, 26 - 30 June, 2016. New York, NY, United States: AIChE.

  • Tokic, M., Hadadi, N., Ataman, M., Miskovic, L., Neves, P., Ebert, B. E., Blank, L. M. and Hatzimanikatis, V. (2016). Discovery and evaluation of novel pathways for production of the second generation of biofuels. 11th Metabolic Engineering Conference 2016, Awaji Island, Japan, 26 - 30 June, 2016. New York, NY, United States: AIChE.

  • Ebert, B. E., Czarnotta, E., Walter, K., Knuf, C., Maury, J., Jacobsen, S. A., Lewandowski, A., Polakowski, T., Lang, C., Forster, J. and Blank, L. M. (2016). Metabolic engineering of saccharomyces cerevisiae for cyclic terpenoid production. 11th Metabolic Engineering Conference 2016, Awaji Island, Japan, 26 - 30 June, 2016. New York, NY, United States: AIChE.

  • Ulonska, Kirsten, Ebert, Birgitta E., Blank, Lars M., Mitsos, Alexander and Viell, Jörn (2015). Systematic screening of fermentation products as future platform chemicals for biofuels. 12th International Symposium on Process Systems Engineering and 25th European Symposium on Computer Aided Process Engineering, Copenhagen, Denmark, 31 May - 4 June 2015. Amsterdam, Netherlands: Elsevier. doi: 10.1016/b978-0-444-63577-8.50067-x

Grants (Administered at UQ)

PhD and MPhil Supervision

Current Supervision

  • Doctor Philosophy — Principal Advisor

    Other advisors:

  • Doctor Philosophy — Principal Advisor

    Other advisors:

Possible Research Projects

Note for students: The possible research projects listed on this page may not be comprehensive or up to date. Always feel free to contact the staff for more information, and also with your own research ideas.

  • This project is embedded in a larger project on plastic waste valorization. In a hybrid approach, we thermo-chemically convert mixed plastic waste into small molecules, which are fed to bacteria for upcycling into biodegradable bioplastic.

    We work with Pseudomonas putida, a soil bacterium capable to grow on a broad variety of carbon sources including most molecules derived from plastic degradation. Your task will be to optimize the microbe for the simultaneous conversion of the substrate mix and the production of polyhydroxyalkanoates. Your tasks include the design of optimal metabolic pathway, the implementation of these designs in vivo via synthetic biology tools, characterization of the engineered strains for substrate conversion and product formation at shake-flask and bioreactor scale. In parallel to the targeted approaches, you will also perform adaptive laboratory evolution experiments to improve the fitness of the microbial strain towards toxic components contained in the plastic waste streams. Sequencing of evolved strains will allow us to identify key mutations, which we will reverse engineer into Pseudomonas.

    You will gain in-depth knowledge on the metabolism of Pseudomonas and practical skills in metabolic engineering and synthetic biology including, molecular biology, omics analyses, microbiological work, fermentation, and analytics.

    Honours and (under)graduate students are welcomed to work on specific subprojects.

    Please contact me for further information.

  • Modern protein-based vaccines require adjuvants to improve immunogenicity and hence efficacy. The natural product class of triterpenoids includes molecules that have been shown to be very potent vaccine adjuvants. From these candidates, squalene and Quillaja saponins have been approved for their use in vaccines against flu, shingles and malaria. And many more triterpenoid-adjuvanted vaccines are in the pipeline.

    These molecules are currently sourced from animal and plant-derived sources. Squalene is found in high abundance in the liver oil from (deep-sea) sharks and currently the only approved source for medical applications. The Quillaja saponins contained in QS-21 adjuvants are only produced by specific trees in limited regions in South America. Both species, sharks and Quillaja saponaria, are threatened by overexploitation. With the increasing demand for potent vaccines, this is expected to increase.

    In this project, we are working on the biotechnological production of these compounds with engineered Baker's yeast Saccharomyces cerevisiae. We can produce squalene and QS-21 precursors at the gram-scale level, which is the current state of the art.

    Within this larger project, two HDR projects are available focusing on (a) improving squalene production and secretion of the intracellular storage molecule into the fermentation medium, and (b) implementing the complex QS-21 biosynthesis pathways in the yeast chassis.

    Honours and (under)graduate students are welcomed to work on specific subprojects.

    You will gain in-depth knowledge on the metabolism of S. cerevisiae and practical skills in metabolic engineering and synthetic biology including, molecular biology, omics analyses, microbiological work, fermentation, and analytics.

    Please contact me for further information.

  • The yeast Saccharomyces cerevisiae is widely used in fermentation to produce wine, beer, and bioethanol. However, this well-researched microbe can also be efficiently engineered for the production of complex natural products. Well-known examples are the anti-malaria drug artemisinin are the ant-cancer drug paclitaxel.

    In this project, we are interested in the production of triterpenoids, the largest group in the natural product class. Many of these molecules have biological activities that make them promising candidates for pharma, nutraceutical, or cosme(ceu)tical applications.

    We have engineered a superior S. cerevisiae platform strain capable of the synthesis of diverse triterpenoids at the gram-scale level. In this project, we aim to expand the product spectrum to alpha-amyrin type triterpenoids with anti-ageing and anti-obesity properties that are used are investigated for use in cosmetics and pharmaceuticals.

    You will recombinantly express plant enzymes in the yeast chassis to enable the production of a few target products. You will further address a major bottleneck in the production of triterpenoids, the intracellular accumulation of the products, which results in cell toxification and low production efficiency. We are following alternative and complementary approaches including the expression of recently identified transporter, in situ extraction and optimization of the intracellular product trafficking route.

    You will gain in-depth knowledge on the metabolism of S. cerevisiae and practical skills in metabolic engineering and synthetic biology including, molecular biology, omics analyses, microscopy, fermentation, and analytics.

    Honours and (under)graduate students are welcomed to work on specific subprojects.

    Please contact me for further information.