Dr Esteban Marcellin's research is focussed on Advance Biomanufacturing and Systems and Synthetic Biology.

Systems biology is a powerful tool to guide the improvement of fermentation processes. It is an important tool used to identify targets for metabolic engineering and to develop new microbial and mammalian production strains. Systems Biology is a knowledge driven approach that takes advantage of the growth in high throughput ‘-omics, (genomics, transcriptomics, proteomics and metabolomics) and uses mathematical models to accelerate learning. The models are functional annotations that can be probed to suggest potential metabolic engineering strategies (e.g. gene targets for knock out/up-regulation) to improve yield and productivity using synthetic biology. The models are refined and validated using biological ‘–omics data, leading to further iterative rounds of metabolic engineering to enhance production. AIBN’s systems and synthetic biology goes beyond conventional ‘omics studies to understand complex cellular behaviours in unconventional microorganisms. For example, using gas fermentation, we are consuming greenhouse gases (CO and CO2) as feedstock for fermentation and converting those greenhouse gases into valuable chemicals and fuels. The technology enables a decrease in our dependence on finite fossil fuel resources and improves sustainability for Australia and the chemical industry. Our projects aim at producing efficient cell lines to increase yields and productivities of mammalian cells lines for biologics production as well as microbial cell factories. In collaboration with leaders in the industry, such as Lanzatech, Amyris, Zoetis, Dow, CSL and Patheon Thermo Fisher we are applying systems metabolic engineering to enhance yields and to increase the production scope of the advanced biomanufacturing sector.

Key publications

Valgepea K, Talbo G, Takemori N, Takemori A, Ludwig C, Mahamkali V, Mueller A, Tappel R, Köpke M, Simpson DS, Nielsen LK, Marcellin E (2022). Absolute Proteome Quantification in the Gas-Fermenting Acetogen Clostridium autoethanogenum. Msystems 7 (2), e00026-22

MacDonald M, Nöbel M, Martínez V, Baker K, Shave E, Gray PP, Mahler S, Munro T, Nielsen LK, Marcellin E (2022). Engineering death resistance in CHO cells for improved perfusion culture. Mabs 14 (1) 2083465

Mahamkali V, Valgepea K, de Souza Pinto Lemgruber R, Plan M, Tappel R, Köpke M, Simpson SD, Nielsen LK, Marcellin E (2020) Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenum. Proceedings of the National Academy of Sciences (PNAS) 117 (23) 13168-13175

Heffernan, J. K., Valgepea, K., Souza, R. De, Lemgruber, P., Casini, I., Plan, M., et al. (2020). Enhancing CO₂-valorization using Clostridium autoethanogenum for sustainable fuel and chemicals production. Front. Bioeng. Biotechnol. 8, 1–10. doi:10.3389/fbioe.2020.00204. 

Marcellin E, Behrendorff JB, Nagaraju S, DeTissera S, Segovia S, Palfreyman R, Daniell J, Licona-Cassani C, Quek L, Speight R, Hodson M, Simpson S, Mitchell W, Köpke M, Nielsen LK. (2016). Low carbon fuels and commodity chemicals from waste gases–Systematic approach to understand energy metabolism in a model acetogen. Green Chemistry 18 (10), 3020-3028


Metabolics and proteomics


Cell factory design studio