Daniel applies genetic engineering, synthetic biology, and systems biology to enhance microbial metabolism for biotechnological applications.
Current biotechnological processes for fine and bulk chemical production rely on refined sugars (e.g., glucose, fructose), creating competition with the global food industry. With global food demand expected to rise by 70% by 2050, sustainable alternatives are essential. To address this challenge, Daniel focuses on the metabolic engineering of Pseudomonas putida to utilize industrial waste streams as alternative feedstocks. His research integrates metabolic modelling to identify novel biosynthetic pathways for assimilating toxic feedstock components and improving carbon yields, enhancing the sustainability of bioprocesses. By engineering a whole-cell biocatalyst capable of using industrial waste as its sole carbon source, his work contributes to the transition toward a circular bioeconomy. Before starting his PhD at AIBN in April 2022, Daniel earned a B.Sc. (2018) and M.Sc. (2021) in Molecular Biotechnology from Bielefeld University, Germany. His research interests in synthetic biology and metabolic engineering began during the 2017 iGEM competition, followed by an industrial internship at Evonik Industries (2018) and a research stay at MIT (2019), where he also encountered the field’s limitations. To address these, he explored FBA-based metabolic modelling by studying synthetic microbial co-cultures for his master’s thesis at the Research Center Jülich (Helmholtz Society, 2020–2021). Additionally, he gained expertise in metabolomics while investigating phosphoregulation of central carbon metabolism in E. coli during a research internship at ETH Zürich (2021–2022).
Collaborations
As part of a joint supervision program between the University of Queensland and the Technical University of Denmark, Daniel is pursuing his PhD under the supervision of Dr. Birgitta Ebert (AIBN), Prof. Dr. Esteban Marcellin (AIBN), and Prof. Dr. Pablo I. Nikel (Novo Nordisk Foundation Center for Biosustainability, DTU, Denmark). His research on redox engineering via inorganic electron donors to improve carbon yields from bioprocesses has led to a collaboration with Prof. Dr. Bastian Blombach’s group at TUM (Germany). Additionally, as a CSIRO top-up scholar at the AEB FSP under Prof. Dr. Robert Speight, Daniel has access to CSIRO facilities to further advance his research.
Funding
Daniel’s research is funded by the highly competitive CSIRO Top-Up Scholarship and Bioplatforms Australia, among others.
Key Publications
Schito S., Zuchowski R., Bergen D., Strohmeier D., Wollenhaupt B., Menke P., Seiffarth J., Nöh K., Kohlheyer D., Bott M., Wiechert W., Baumgart M., Noack S. Communities of Niche-optimized Strains (CoNoS) - Design and creation of stable, genome-reduced co-cultures. Metab Eng. 2022, 73, 91-103 (Sep 2022). doi: 10.1016/j.ymben.2022.06.004.
Bergen D., Puiggené Ò., Marcellin E., Speight R. E., Nikel P. I., Ebert B. E. Co-Substrate Free Valorisation of Lignin Monomers by Assimilation of C1 and C2 By-Products. bioRxive.
Puiggené Ò., Muñoz-Triviño J., Civil-Ferrer L., Gille L., Schulz-Mirbach H., Bergen D., Erb T. J., Ebert B. E., Nikel P. I. Systematic engineering of synthetic serine cycles in Pseudomonas putida uncovers emergent topologies for methanol assimilation. bioRxive.
Bergen D., Nikel P. I., Marcellin E., Ebert B. E. Model-Based Identification of Synthetic C1 Assimilation Pathways for the Efficient Valorisation of Lignin-Derived Compounds. Presented at CoESB Conference 2022 (Kingscliff, Australia), CoESB Conference 2023 (Sunshine Coast, Australia), and SBA Conference 2023 (Perth, Australia).
Bergen D., Marcellin E., Speight R., Nikel P. I., Ebert B. E. Boosting Carbon Efficiency of Bioprocesses Using Hydrogen-Powered Whole Cell Biocatalysts. Presented at Gas Fermentation Conference 2024 (Gladstone, Australia).