Synthetic Ecology

Our group has previously applied high-throughput sequencing technologies for finding the underlying molecular mechanisms for improved microbial carbon source utilization, increased product formation, and stress tolerance. We used mainly Saccharomyces cerevisiae and Aspergilli as cell factories of added- and high added- value molecules and we integrate –omic data with flux balance analysis for mapping industrially relevant genotype-to-phenotype links including exploiting natural diversity in natural isolates or crosses between isolates, classical mutagenesis and evolutionary engineering.

Currently, our group is working on the rational gain of function engineering of bacteria and fungi that would allow the development of complex, safe and successful clinical applications of microorganisms especially for in-situ compound production in the human gut. Using microorganisms overproducing certain metabolites that restore immune homeostasis or creating the most efficient synthetic communities to fight abdominal infections holds great potential as long as we improve the quality of evidence and regulation of their use. We are focusing on understanding the microbial metabolic interdependencies for developing the computational framework that enables the design of microbiome engineering-based prophylactic and therapeutic interventions.


Xiuqiang (Stephen) Chen
Mohammadhassan Mirhakkak Esfahani
Sascha Schäuble


Marfil-Sánchez A*, Zhang L*, Alonso-Pernas P, Mirhakkak M, Mueller M, Seelbinder B, Ni Y, Santhanam R, Busch A, Beemelmanns C, Ermolaeva M, Bauer M#, Panagiotou G# (2021) An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness. Gut Microbes 13(1), 1993598.
Mirhakkak M, Schäuble S, Klassert T, Brunke S, Brandt P, Loos D, Uribe R, de Oliveira Lino FS, Ni Y, Vylkova S, Slevogt H, Hube B, Weiss G, Sommer M, Panagiotou G# (2021) Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels. ISME J 15(5), 1257-1270.
Kang K, Bergdahl B, Machado D, Dato L, Han TL, Li J, Villas-Boas S, Herrgård MJ, Förster J, Panagiotou G (2019) Linking genetic, metabolic and phenotypic diversity among S. cerevisiae strains using multi-omics associations Gigascience 8(4), giz015.
Heshiki Y, Dissanayake T, Zheng T, Kang K, Yueqiong N, Xu Z, Sarkar C, Woo PCY, Chow BKC, Baker D, Yan A, Webster CJ, Panagiotou G**, Li J** (2017) Toward a Metagenomic Understanding on the Bacterial Composition and Resistome in Hong Kong Banknotes. Front Microbiol 8, 632.