Microbial Genomics and Biodegradation

Our research asks a simple question with a difficult answer: how do microorganisms break down the chemicals that humans release into the environment, and how can we put that ability to work? We work at the interface of molecular microbiology, bioinformatics, and protein science.

Environmental DNA and metagenome sequencing let us search microbial communities from polluted sites for the organisms and genes behind degradation of xenobiotics – including the rare enzymatic chemistry needed to break the carbon–fluorine bond in PFAS. Candidate genes are then moved into the laboratory, expressed, and characterised biochemically on real pollutants.

Pollutants are not only substrates but also stressors, and a second line of work concerns the toxic effects of pollutants on microorganisms: how exposure shapes growth, physiology, community composition, and the selection of catabolic traits.

Sequence and screening data feed into state-of-the-art protein–ligand modelling. Combining structure prediction, molecular docking, molecular dynamics, and machine learning, we model how candidate enzymes bind and process pollutant molecules, prioritise the most promising variants for testing, and design improved ones – shortening the route from a gene found in nature to an enzyme that works.

Teaching is part of the research. We integrate our own research questions into our teaching, so students work on genuine, unanswered problems with real samples and real data. This often leads on to student projects and theses building on what began in the course. Interested in joining us for a thesis project? Contact Tue at tkn@plen.ku.dk and discuss your own idea or hear more about what projects are available.