Synthetic Ecology

The application of genome-scale technologies, both experimental and in silico, to industrial biotechnology has allowed improving the conversion of biomass-derived feedstocks to chemicals, materials and fuels through microbial fermentation. Our group applied high-throughput sequencing technologies for finding the underlying molecular mechanisms for improved 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. The efficacy of live microorganisms in the prevention and treatment of diseases has been extensively studied by academics and industry. Despite the often opposing conclusions for their prophylactic and therapeutic health indications 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.