Birgitta Ebert’s research focuses on developing biotechnology concepts to address critical challenges such as pollution, climate change and overexploitation of natural resources.
She specializes in improving microbial catalysts for eco-friendly chemical and material production by leveraging metabolic engineering, synthetic biology, systems analysis, and modelling. Her goal is to create microbial cell factories that convert renewable resources and waste into valuable products, reducing reliance on petrochemicals. She collaborates closely with chemists and chemical engineers to enhance the integration of chemical and biological processes for improved efficiency and sustainability.
Birgitta has a background in Chemical Engineering and a PhD in Systems Biotechnology from TU Dortmund University (Germany). She led a research group in Systems Metabolic Engineering at the Institute of Applied Microbiology at RWTH Aachen University (Germany) from 2012 to 2019. In 2016, she expanded her expertise in Synthetic Biology by joining the Keasling lab at the University of California in Berkeley and the Joint BioEnergy Institute in Emeryville (USA).
Since April 2019, she has been at the Australian Institute for Bioengineering and Nanotechnology at the University of Queensland, applying her expertise to engineer microbial cell factories for fermentation-based manufacturing.
Journal Article: Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose
Dvořák, Pavel, Burýšková, Barbora, Popelářová, Barbora, Ebert, Birgitta E., Botka, Tibor, Bujdoš, Dalimil, Sánchez-Pascuala, Alberto, Schöttler, Hannah, Hayen, Heiko, de Lorenzo, Víctor, Blank, Lars M. and Benešík, Martin (2024). Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose. Nature Communications, 15 (1) 2666. doi: 10.1038/s41467-024-46812-9
Journal Article: Expanding Pseudomonas taiwanensis VLB120's acyl‐CoA portfolio: propionate production in mineral salt medium
Neves, Dário, Meinen, Daniel, Alter, Tobias B., Blank, Lars M. and Ebert, Birgitta E. (2023). Expanding Pseudomonas taiwanensis VLB120's acyl‐CoA portfolio: propionate production in mineral salt medium. Microbial Biotechnology, 17 (1) e14309, e14309. doi: 10.1111/1751-7915.14309
Journal Article: Cross-species synthetic promoter library: finding common ground between Pseudomonas taiwanensis VLB120 and Escherichia coli
Neves, Dário, Liebal, Ulf W., Nies, Salome C., Alter, Tobias B., Pitzler, Christian, Blank, Lars M. and Ebert, Birgitta E. (2023). Cross-species synthetic promoter library: finding common ground between Pseudomonas taiwanensis VLB120 and Escherichia coli. ACS Synthetic Biology, 12 (7), 2029-2040. doi: 10.1021/acssynbio.3c00084
ARC Research Hub for Carbon Utilisation and Recycling (ARC ITRP administered by Monash University)
(2023–2028) Monash University
(2023–2025) NHMRC IDEAS Grants
Chemo-biocatalytic conversion of lignin to high-performance fibre monomers
(2023–2024) United States Army International Technology Center-Pacific (ITC-PAC)
(2023) Doctor Philosophy
Co-assimilation of C1 compounds (methanol, formate, formaldehyde) and components from lignocellulosic feedstock
Doctor Philosophy
Understanding terpenoid metabolism in cyanobacteria
(2022) Doctor Philosophy
Brewing natural products with yeast
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.
Vaccine adjuvant production in tailored yeast
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.
Redox engineering for carbon-efficient biotechnological processes
Redox cofactors play a central role in the metabolism of living organisms. The most widely used cofactor is NAD(P)H. In the central carbon metabolism, the oxidised form NAD(P)+ is the primary acceptor for electrons from carbon oxidation. These electrons are then fed into the electron transfer chain, powering the respiratory system for ATP and thus energy generation. Although efficient, this system leads to CO2 formation via the oxidation of carbon metabolites and, hence, to CO2 emissions during biotechnological processes. In this project, we investigate alternative systems for NADH regeneration with electrons from sustainable energy sources, ultimately decoupling energy and carbon metabolism. Our focus lies hereby on hydrogenases. These enzymes use electrons from hydrogen to generate NADH instead of carbon metabolites, while hydrogen can be produced solely from water and electrons from renewable energy sources. Implementing efficient hydrogenase-based NADH regeneration systems in vivo should lead to more carbon-efficient and sustainable biotechnological processes for a greener bio-based future.
We’re looking for a motivated student interested in carbon-efficient biological processes. The project offers options for working in molecular biology, bioprocess development, and robotics. Please get in touch with me for further information.
Microbial production, extraction, and quantitative analysis of isoprenoids
Satta, Alessandro, Lu, Zeyu, Plan, Manuel R., Esquirol, Lygie and Ebert, Birgitta E. (2022). Microbial production, extraction, and quantitative analysis of isoprenoids. Plant Secondary Metabolism Engineering: methods and protocols.. (pp. 239-259) New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-2185-1_20
Halbfeld, Christoph, Baumbach, Jörg Ingo, Blank, Lars M. and Ebert, Birgitta E. (2018). Multi-capillary column ion mobility spectrometry of volatile metabolites for phenotyping of microorganisms. Synthetic metabolic pathways: methods and protocols. (pp. 229-258) New York, NY, United States: Humana Press. doi: 10.1007/978-1-4939-7295-1_15
GC-MS-Based Determination of Mass Isotopomer Distributions for 13C-Based Metabolic Flux Analysis
Schmitz, Andreas, Ebert, Birgitta E. and Blank, Lars M. (2015). GC-MS-Based Determination of Mass Isotopomer Distributions for 13C-Based Metabolic Flux Analysis. Hydrocarbon and lipid microbiology protocols: genetic, genomic and system analyses of pure cultures. (pp. 223-243) edited by Terry J. McGenity, Kenneth N. Timmis and Balbina Nogales. Berlin, Heidelberg: Springer Berlin Heidelberg. doi: 10.1007/8623_2015_78
Successful downsizing for high-throughput 13C-MFA applications
Ebert, Birgitta E. and Blank, Lars M. (2014). Successful downsizing for high-throughput 13C-MFA applications. In Jens O. Krömer, Lars K. Nielsen and Lars M. Blank (Ed.), Metabolic flux analysis: methods and protocols (pp. 127-142) New York, NY, United States: Humana Press. doi:10.1007/978-1-4939-1170-7_8
Energy and cofactor issues in fermentation and oxyfunctionalization processes
Bühler, Bruno, Blank, Lars M., Ebert, Birgitta E., Bühler, Katja and Schmid, Andreas (2009). Energy and cofactor issues in fermentation and oxyfunctionalization processes. The Metabolic Pathway Engineering Handbook: Tools and Applications. (pp. 21-1-21-32) CRC Press.
Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose
Dvořák, Pavel, Burýšková, Barbora, Popelářová, Barbora, Ebert, Birgitta E., Botka, Tibor, Bujdoš, Dalimil, Sánchez-Pascuala, Alberto, Schöttler, Hannah, Hayen, Heiko, de Lorenzo, Víctor, Blank, Lars M. and Benešík, Martin (2024). Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose. Nature Communications, 15 (1) 2666. doi: 10.1038/s41467-024-46812-9
Neves, Dário, Meinen, Daniel, Alter, Tobias B., Blank, Lars M. and Ebert, Birgitta E. (2023). Expanding Pseudomonas taiwanensis VLB120's acyl‐CoA portfolio: propionate production in mineral salt medium. Microbial Biotechnology, 17 (1) e14309, e14309. doi: 10.1111/1751-7915.14309
Neves, Dário, Liebal, Ulf W., Nies, Salome C., Alter, Tobias B., Pitzler, Christian, Blank, Lars M. and Ebert, Birgitta E. (2023). Cross-species synthetic promoter library: finding common ground between Pseudomonas taiwanensis VLB120 and Escherichia coli. ACS Synthetic Biology, 12 (7), 2029-2040. doi: 10.1021/acssynbio.3c00084
Guo, Hao, Wang, Huiyan, Chen, Tongtong, Guo, Liwei, Blank, Lars M., Ebert, Birgitta E. and Huo, Yi-Xin (2023). Correction to “Engineering Critical Amino Acid Residues of Lanosterol Synthase to Improve the Production of Triterpenoids in Saccharomyces cerevisiae”. ACS Synthetic Biology, 12 (4), 1377-1377. doi: 10.1021/acssynbio.3c00142
Non-invasive monitoring of microbial triterpenoid production using nonlinear microscopy techniques
Dianat, Mariam, Münchberg, Ute, Blank, Lars M., Freier, Erik and Ebert, Birgitta E. (2023). Non-invasive monitoring of microbial triterpenoid production using nonlinear microscopy techniques. Frontiers in Bioengineering and Biotechnology, 11 1106566, 1-12. doi: 10.3389/fbioe.2023.1106566
Current metabolic engineering strategies for photosynthetic bioproduction in cyanobacteria
Satta, Alessandro, Esquirol, Lygie and Ebert, Birgitta E. (2023). Current metabolic engineering strategies for photosynthetic bioproduction in cyanobacteria. Microorganisms, 11 (2) 455. doi: 10.3390/microorganisms11020455
Satta, Alessandro, Esquirol, Lygie, Ebert, Birgitta E., Newman, Janet, Peat, Thomas S., Plan, Manuel, Schenk, Gerhard and Vickers, Claudia E. (2022). Molecular characterization of cyanobacterial short‐chain prenyltransferases and discovery of a novel GGPP phosphatase. The FEBS Journal, 289 (21), 6672-6693. doi: 10.1111/febs.16556
Vinde, Marcos H., Cao, Da, Chesterfield, Rebecca J., Yoneyama, Kaori, Gumulya, Yosephine, Thomson, Raine E. S., Matila, Tebogo, Ebert, Birgitta E., Beveridge, Christine A., Vickers, Claudia E. and Gillam, Elizabeth M. J. (2022). Ancestral sequence reconstruction of the CYP711 family reveals functional divergence in strigolactone biosynthetic enzymes associated with gene duplication events in monocot grasses. New Phytologist, 235 (5), 1900-1912. doi: 10.1111/nph.18285
Guo, Hao, Wang, Huiyang, Chen, Tongtong, Guo, Liwei, Blank, Lars M., Ebert, Birgitta E. and Huo, Yi-Xin (2022). Engineering critical amino acid residues of lanosterol synthase to improve the production of triterpenoids in Saccharomyces cerevisiae. ACS Synthetic Biology, 11 (8), 2685-2696. doi: 10.1021/acssynbio.2c00098
Wefelmeier, Katrin, Ebert, Birgitta E., Blank, Lars M. and Schmitz, Simone (2022). Mix and match: promoters and terminators for tuning gene expression in the methylotrophic yeast Ogataea polymorpha. Frontiers in Bioengineering and Biotechnology, 10 876316, 1-14. doi: 10.3389/fbioe.2022.876316
Auxin-mediated protein depletion for metabolic engineering in terpene-producing yeast
Lu, Zeyu, Peng, Bingyin, Ebert, Birgitta E., Dumsday, Geoff and Vickers, Claudia E. (2021). Auxin-mediated protein depletion for metabolic engineering in terpene-producing yeast. Nature Communications, 12 (1) 1051, 1051. doi: 10.1038/s41467-021-21313-1
Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha
Liebal, Ulf W., Fabry, Brigida A., Ravikrishnan, Aarthi, Schedel, Constantin V. l., Schmitz, Simone, Blank, Lars M. and Ebert, Birgitta E. (2021). Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha. BMC Biotechnology, 21 (1) 23, 23. doi: 10.1186/s12896-021-00675-w
Hayat, Irfan Farabi, Plan, Manuel, Ebert, Birgitta E., Dumsday, Geoff, Vickers, Claudia E. and Peng, Bingyin (2021). Auxin‐mediated induction of GAL promoters by conditional degradation of Mig1p improves sesquiterpene production in Saccharomyces cerevisiae with engineered acetyl‐CoA synthesis. Microbial Biotechnology, 14 (6) 1751-7915.13880, 1-16. doi: 10.1111/1751-7915.13880
Proteome regulation patterns determine Escherichia coli wild-type and mutant phenotypes
Alter, Tobias B., Blank, Lars M. and Ebert, Birgitta E. (2021). Proteome regulation patterns determine Escherichia coli wild-type and mutant phenotypes. mSystems, 6 (2) e00625-20. doi: 10.1128/msystems.00625-20
Dahlin, Jonathan, Holkenbrink, Carina, Marella, Eko Roy, Wang, Guokun, Liebal, Ulf, Lieven, Christian, Weber, Dieter, McCloskey, Douglas, Wang, Hong-Lei, Ebert, Birgitta E., Herrgård, Markus J., Blank, Lars Mathias and Borodina, Irina (2021). Corrigendum: Multi-Omics Analysis of Fatty Alcohol Production in Engineered Yeasts Saccharomyces cerevisiae and Yarrowia lipolytica (Front Genet, (2019), 10, (747), 10.3389/fgene.2019.00747). Frontiers in Genetics, 11 637738, 1-2. doi: 10.3389/fgene.2020.637738
High titer methyl ketone production with tailored Pseudomonas taiwanensis VLB120
Nies, Salome C., Alter, Tobias B., Nölting, Sophia, Thiery, Susanne, Phan, An N.T., Drummen, Noud, Keasling, Jay D., Blank, Lars M. and Ebert, Birgitta E. (2020). High titer methyl ketone production with tailored Pseudomonas taiwanensis VLB120. Metabolic Engineering, 62, 84-94. doi: 10.1016/j.ymben.2020.08.003
Nies, Salome C., Dinger, Robert, Chen, Yan, Wordofa, Gossa G., Kristensen, Mette, Schneider, Konstantin, Büchs, Jochen, Petzold, Christopher J., Keasling, Jay D., Blank, Lars M. and Ebert, Birgitta E. (2020). A systems analysis of NADH dehydrogenase mutants reveals flexibility and limits of Pseudomonas taiwanensis VLB120's metabolism. Applied and Environmental Microbiology, 86 (11) 3819. doi: 10.1128/aem.03038-19
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian, Beber, Moritz E., Olivier, Brett G., Bergmann, Frank T., Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A., Blank, Lars M., Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E., Edirisinghe, Janaka N., Faria, José P., Feist, Adam M., Fengos, Georgios, Fleming, Ronan M. T., García-Jiménez, Beatriz, Hatzimanikatis, Vassily, van Helvoirt, Wout, Henry, Christopher S., Hermjakob, Henning, Herrgård, Markus J., Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda ... Zhang, Cheng (2020). Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology, 38 (4), 504-504. doi: 10.1038/s41587-020-0477-4
MEMOTE for standardized genome-scale metabolic model testing
Lieven, Christian, Beber, Moritz E., Olivier, Brett G., Bergmann, Frank T., Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A., Blank, Lars M., Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E., Edirisinghe, Janaka N., Faria, José P., Feist, Adam M., Fengos, Georgios, Fleming, Ronan M. T., García-Jiménez, Beatriz, Hatzimanikatis, Vassily, van Helvoirt, Wout, Henry, Christopher S., Hermjakob, Henning, Herrgård, Markus J., Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda ... Zhang, Cheng (2020). MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology, 38 (3), 272-276. doi: 10.1038/s41587-020-0446-y
Neves, Dário, Vos, Stefan, Blank, Lars M. and Ebert, Birgitta E. (2020). Pseudomonas mRNA 2.0: Boosting gene expression through enhanced mRNA stability and translational efficiency. Frontiers in Bioengineering and Biotechnology, 7 458, 458. doi: 10.3389/fbioe.2019.00458
Rockenbach, Alexander, Sudarsan, Suresh, Berens, Judith, Kosubek, Michael, Lazar, Jaroslav, Demling, Philipp, Hanke, René, Mennicken, Philip, Ebert, Birgitta E., Blank, Lars M. and Schnakenberg, Uwe (2019). Microfluidic irreversible electroporation — a versatile tool to extract intracellular contents of bacteria and yeast. Metabolites, 9 (10) 211, 211. doi: 10.3390/metabo9100211
Dahlin, Jonathan, Holkenbrink, Carina, Morella, Eko Roy, Wang, Guokun, Liebal, Ulf, Lieven, Christian, Weber, Dieter, McCloskey, Douglas, Ebert, Birgitta E., Herrgard, Markus J., Blank, Lars Mathias and Borodina, Irina (2019). Multi-omics analysis of fatty alcohol production in engineered yeasts Saccharomyces cerevisiae and Yarrowia lipolytica. Frontiers in Genetics, 10 (JUL) 747. doi: 10.3389/fgene.2019.00747
Zahoor, Ahmed, Küttner, Felix T. F., Blank, Lars M. and Ebert, Birgitta E. (2019). Evaluation of pyruvate decarboxylase‐negative Saccharomyces cerevisiae strains for the production of succinic acid. Engineering in Life Sciences, 19 (10) elsc.201900080, 711-720. doi: 10.1002/elsc.201900080
Determination of growth-coupling strategies and their underlying principles
Alter, Tobias B. and Ebert, Birgitta E. (2019). Determination of growth-coupling strategies and their underlying principles. BMC Bioinformatics, 20 (1) 447, 447. doi: 10.1186/s12859-019-2946-7
Lehnen, Mathias, Ebert, Birgitta E. and Blank, Lars M. (2019). Elevated temperatures do not trigger a conserved metabolic network response among thermotolerant yeasts. BMC Microbiology, 19 (1) 100, 100. doi: 10.1186/s12866-019-1453-3
Jessop‐Fabre, Mathew M, Dahlin, Jonathan, Biron, Mathias B, Stovicek, Vratislav, Ebert, Birgitta E, Blank, Lars M, Budin, Itay, Keasling, Jay D and Borodina, Irina (2019). The transcriptome and flux profiling of Crabtree‐negative hydroxy acid producing strains of Saccharomyces cerevisiae reveals changes in the central carbon metabolism. Biotechnology Journal, 14 (9) 1900013, 1900013. doi: 10.1002/biot.201900013
Aromatisation of bio-derivable isobutyraldehyde over HZSM-5 zeolite catalysts
Deischter, Jeff, Schute, Kai, Neves, Dario S., Ebert, Brigitta E., Blank, Lars M. and Palkovits, Regina (2019). Aromatisation of bio-derivable isobutyraldehyde over HZSM-5 zeolite catalysts. Green Chemistry, 21 (7), 1710-1717. doi: 10.1039/c9gc00483a
CO2 to succinic acid – Estimating the potential of biocatalytic routes
Liebal, Ulf W., Blank, Lars M. and Ebert, Birgitta E. (2018). CO2 to succinic acid – Estimating the potential of biocatalytic routes. Metabolic Engineering Communications, 7 e00075, e00075. doi: 10.1016/j.mec.2018.e00075
Tokic, Milenko, Hadadi, Noushin, Ataman, Meric, Neves, Dário, Ebert, Birgitta E., Blank, Lars M., Miskovic, Ljubisa and Hatzimanikatis, Vassily (2018). Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors. ACS Synthetic Biology, 7 (8), 1858-1873. doi: 10.1021/acssynbio.8b00049
A breath of information: the volatilome
Mansurova, M., Ebert, Birgitta E., Blank, Lars M. and Ibáñez, Alfredo J. (2018). A breath of information: the volatilome. Current Genetics, 64 (4), 959-964. doi: 10.1007/s00294-017-0800-x
Ebert, Birgitta E, Czarnotta, Eik and Blank, Lars M (2018). Physiologic and metabolic characterization of Saccharomyces cerevisiae reveals limitations in the synthesis of the triterpene squalene. FEMS Yeast Research, 18 (8) foy077. doi: 10.1093/femsyr/foy077
Genetic Optimization Algorithm for Metabolic Engineering Revisited
Alter, Tobias, Blank, Lars and Ebert, Birgitta (2018). Genetic Optimization Algorithm for Metabolic Engineering Revisited. Metabolites, 8 (2) 33, 33. doi: 10.3390/metabo8020033
Lehnen, Mathias, Ebert, Birgitta E. and Blank, Lars M. (2017). A comprehensive evaluation of constraining amino acid biosynthesis in compartmented models for metabolic flux analysis. Metabolic Engineering Communications, 5, 34-44. doi: 10.1016/j.meteno.2017.07.001
Comprehensive real-time analysis of the yeast volatilome
Tejero Rioseras, Alberto, Garcia Gomez, Diego, Ebert, Birgitta E., Blank, Lars M., Ibáñez, Alfredo J. and Sinues, Pablo M.-L. (2017). Comprehensive real-time analysis of the yeast volatilome. Scientific Reports, 7 (1) 14236, 14236. doi: 10.1038/s41598-017-14554-y
Czarnotta, Eik, Dianat, Mariam, Korf, Marcel, Granica, Fabian, Merz, Juliane, Maury, Jerome, Jacobsen, Simo A. Baallal, Forster, Jochen, Ebert, Birgitta E. and Blank, Lars M. (2017). Fermentation and purification strategies for the production of betulinic acid and its lupane-type precursors in Saccharomyces cerevisiae. Biotechnology and Bioengineering, 114 (11), 2528-2538. doi: 10.1002/bit.26377
Exploration and exploitation of the yeast volatilome
Ebert, Birgitta E., Halbfeld, Christoph and Blank, Lars M. (2017). Exploration and exploitation of the yeast volatilome. Current Metabolomics, 5 (2), 102-118. doi: 10.2174/2213235X04666160818151119
Metabolic response of Pseudomonas putida to increased NADH regeneration rates
Zobel, Sebastian, Kuepper, Jannis, Ebert, Birgitta, Wierckx, Nick and Blank, Lars M. (2017). Metabolic response of Pseudomonas putida to increased NADH regeneration rates. Engineering in Life Sciences, 17 (1), 47-57. doi: 10.1002/elsc.201600072
Metabolic Engineering von Saccharomyces cerevisiaefür die Produktion zyklischer Triterpenoide
Ebert, B. E., Walter, K., Czarnotta, E., Blank, L. M., Förster, J., Lang, C., Knuf, C., Maury, J., Baallal Jacobsen, S. A., Lewandowski, A. and Polakowski, T. (2016). Metabolic Engineering von Saccharomyces cerevisiaefür die Produktion zyklischer Triterpenoide. Chemie Ingenieur Technik, 88 (9), 1393-1393. doi: 10.1002/cite.201650466
Kildegaard, Kanchana R., Jensen, Niels B., Schneider, Konstantin, Czarnotta, Eik, Oezdemir, Emre, Klein, Tobias, Maury, Jerome, Ebert, Birgitta E., Christensen, Hanne B., Chen, Yun, Kim, Il-Kwon, Herrgard, Markus J., Blank, Lars M., Forster, Jochen, Nielsen, Jens and Borodina, Irina (2016). Engineering and systems-level analysis of Saccharomyces cerevisiae for production of 3-hydroxypropionic acid via malonyl-CoA reductase-dependent pathway. Microbial Cell Factories, 15 (1) 53. doi: 10.1186/s12934-016-0451-5
Balakumaran, Palanisamy Athiyaman, Foerster, Jan, Zimmermann, Martin, Charumathi, Jayachandran, Schmitz, Andreas, Czarnotta, Eik, Lehnen, Mathias, Sudarsan, Suresh, Ebert, Birgitta E., Blank, Lars Mathias and Meenakshisundaram, Sankaranarayanan (2016). The trade-off of availability and growth inhibition through copper for the production of copper-dependent enzymes by Pichia pastoris. BMC Biotechnology, 16 (1) 20. doi: 10.1186/s12896-016-0251-3
Halbfeld, Christoph, Ebert, Birgitta E. and Blank, Lars M. (2014). Multi-capillary column-ion mobility spectrometry of volatile metabolites emitted by Saccharomyces cerevisiae. Metabolites, 4 (3), 751-774. doi: 10.3390/metabo4030751
From measurement to implementation of metabolic fluxes
Blank, Lars M. and Ebert, Birgitta E. (2013). From measurement to implementation of metabolic fluxes. Current Opinion in Biotechnology, 24 (1), 13-21. doi: 10.1016/j.copbio.2012.10.019
Flux-P: automating metabolic flux analysis
Ebert, Birgitta E., Lamprecht, Anna-Lena, Steffen, Bernhard and Blank, Lars M. (2012). Flux-P: automating metabolic flux analysis. Metabolites, 2 (4), 872-890. doi: 10.3390/metabo2040872
Response of Pseudomonas putida KT2440 to Increased NADH and ATP Demand
Ebert, Birgitta E., Kurth, Felix, Grund, Marcel, Blank, Lars M. and Schmid, Andreas (2011). Response of Pseudomonas putida KT2440 to Increased NADH and ATP Demand. Applied and Environmental Microbiology, 77 (18), 6597-6605. doi: 10.1128/AEM.05588-11
Redox biocatalysis and metabolism: molecular mechanisms and metabolic network analysis
Blank, Lars M., Ebert, Birgitta E., Buehler, Katja and Bühler, Bruno (2010). Redox biocatalysis and metabolism: molecular mechanisms and metabolic network analysis. Antioxidants & Redox Signaling, 13 (3), 349-394. doi: 10.1089/ars.2009.2931
Blank, Lars M., Ionidis, Georgios, Ebert, Birgitta E., Bühler, Bruno and Schmid, Andreas (2008). Metabolic response of Pseudomonas putida during redox biocatalysis in the presence of a second octanol phase : Metabolic response of P. putida to organic solvents. FEBS Journal, 275 (20), 5173-5190. doi: 10.1111/j.1742-4658.2008.06648.x
Blank, Lars M., Ebert, Birgitta E., Buehler, Bruno and Schmid, Andreas (2008). Metabolic capacity estimation of Escherichia coli as a platform for redox biocatalysis: Constraint-based modeling and experimental verification. Biotechnology and Bioengineering, 100 (6), 1050-1065. doi: 10.1002/bit.21837
Development of mini-bioreactors for evolution of thermotolerance
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.
Discovery and evaluation of novel pathways for production of the second generation of biofuels
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.
Metabolic engineering of saccharomyces cerevisiae for cyclic terpenoid production
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.
Systematic screening of fermentation products as future platform chemicals for biofuels
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
ARC Research Hub for Carbon Utilisation and Recycling (ARC ITRP administered by Monash University)
(2023–2028) Monash University
(2023–2025) NHMRC IDEAS Grants
Chemo-biocatalytic conversion of lignin to high-performance fibre monomers
(2023–2024) United States Army International Technology Center-Pacific (ITC-PAC)
(2023–2024) Universities Australia - Germany Joint Research Co-operation Scheme
Production of biopolymers from plastic waste
(2021–2022) Innovation Connections
Co-assimilation of C1 compounds (methanol, formate, formaldehyde) and components from lignocellulosic feedstock
Doctor Philosophy — Principal Advisor
Other advisors:
Exploiting plant biosynthesis to produce vaccine adjuvants
Doctor Philosophy — Principal Advisor
Other advisors:
Development of efficient methods for conversion of plastic waste into high value carbon fibres
Doctor Philosophy — Associate Advisor
Other advisors:
(2023) Doctor Philosophy — Principal Advisor
Other advisors:
Understanding terpenoid metabolism in cyanobacteria
(2022) Doctor Philosophy — Principal Advisor
Other advisors:
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.
Brewing natural products with yeast
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.
Vaccine adjuvant production in tailored yeast
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.
Redox engineering for carbon-efficient biotechnological processes
Redox cofactors play a central role in the metabolism of living organisms. The most widely used cofactor is NAD(P)H. In the central carbon metabolism, the oxidised form NAD(P)+ is the primary acceptor for electrons from carbon oxidation. These electrons are then fed into the electron transfer chain, powering the respiratory system for ATP and thus energy generation. Although efficient, this system leads to CO2 formation via the oxidation of carbon metabolites and, hence, to CO2 emissions during biotechnological processes. In this project, we investigate alternative systems for NADH regeneration with electrons from sustainable energy sources, ultimately decoupling energy and carbon metabolism. Our focus lies hereby on hydrogenases. These enzymes use electrons from hydrogen to generate NADH instead of carbon metabolites, while hydrogen can be produced solely from water and electrons from renewable energy sources. Implementing efficient hydrogenase-based NADH regeneration systems in vivo should lead to more carbon-efficient and sustainable biotechnological processes for a greener bio-based future.
We’re looking for a motivated student interested in carbon-efficient biological processes. The project offers options for working in molecular biology, bioprocess development, and robotics. Please get in touch with me for further information.
Subcellular compartment engineering for improved biocatalytic performance of yeasts.
Research in the Eberg group is developing biotechnological production of valuable plant natural products in Saccharomyces cerevisiae, an established biotechnological workhorse. We are specifically interested in triterpenoids, plant natural products that find applications as high-intensity sweeteners, vaccine adjuvants or cosmetic ingredients and are heavily researched as novel drugs against cancer and other diseases. Our research is driven by the risk of overexploitation of rare plants for product extractions and a need to produce these valuable compounds at higher quantities with efficient and sustainable processes.
Several student projects are available addressing the limitations of establishing triterpenoid production in S. cerevisiae.
1. Enhancement of ER proliferation in Saccharomyces cerevisiae
The project's primary objective is to enhance the amount of endoplasmic reticulum (ER) membrane in the yeast Saccharomyces cerevisiae through metabolic engineering. Triterpenoid synthesis is catalysed by ER membrane-bound enzymes, and our research showed that ER membrane availability limits their production. Building on these initial results, this project shall investigate optimal ER membrane proliferation to maximise productivity.
Genes identified to affect ER proliferation shall be overexpressed or deleted in the yeast engineered for triterpenoid production. This project will expose the student to various molecular biology methods, including plasmid construction, yeast transformation, and CRISPR-Cas9 for gene deletions and insertions. To visualise the ER, fluorescent protein-tagged ER transmembrane protein will be expressed in engineered yeasts. Flow cytometry analysis and confocal microscopy will be employed to compare the ER size of engineered yeast strains and their reference, and the impact of ER size on triterpenoid production will be investigated.
2. Interaction between ER size and broader metabolism of Saccharomyces cerevisiae
Previous studies, which increased ER proliferation to boost triterpenoid production, indicate the manifestation of broader metabolic and phenotypic changes in the engineered yeast strains. To investigate the impact of organelle morphology on cellular biosynthetic pathways, this project will apply proteomics and transcriptomics analysis of strains with diverse ER and cellular phenotypes. The generated comprehensive omics dataset will then be analysed with computational methods to understand better the potential relationship between metabolic pathways and ER membrane proliferation in yeast. These analyses shall also identify innovative, novel engineering targets to augment ER proliferation and triterpenoid production.