Systems Environmental Microbiology

Building synthetic metabolism to make novel molecules (e.g. organohalogens) in environmental bacteria for a sustainable future.

Smart metabolic engineering strategies are urgently needed to tackle current limitations of bio-based production. Our team creates and assembles novel (synthetic) metabolism to explore bio-production beyond Nature’s restrictions, instead of merely collecting known pathways and enzymes to produce a few simple molecules.

The Systems Environmental Microbiology (SEM) group expands bio-production beyond Nature’s boundaries by exploiting unique characteristics of Pseudomonas putida, a non-pathogenic environmental bacterium that we use as a cell factory.



We aim at increasing the type, number and nature of chemicals produced in engineered microbes by rationally incorporating non-biological atoms into the «metabolic agenda» of environmental bacteria. Adding fluorine and other halogens to organic molecules is a widespread strategy for producing added-value halogenated compounds (i.e. organic molecules containing atoms from Group 17 in the periodic table; often also referred to as organohalogens).

Alas, producing organohalogens today exclusively relies on traditional chemistry approaches that are often unselective, requiring difficult-to-handle reagents under harsh operating conditions. To tackle these challenges, we adopt a combination of advanced synthetic biology techniques for bacterial genome edition, automated enzyme discovery and design, deep learning-guided analysis of bacterial metabolism and high-throughput analytics.

Synthetic metabolism

By engineering synthetic metabolism for biosynthesis of organohalogens, the Systems Environmental Microbiology group provides efficient routes to the production of pharma drugs, polymers and industrial chemicals, impacting key areas of everyday life and technology. Our ultimate ambition is to pave the way towards truly sustainable bioproduction of added-value products that have been out of Nature’s reach thus far.

The Systems Environmental Microbiology group is located at The Novo Nordisk Foundation Center for Biosustainability at DTU Lyngby, DTU Biosustain, and it is headed by Senior Researcher Pablo I. Nikel