Microbial Bioengineering

Systems Biology is based on an integrative approach and applies various computational strategies to integrate heterogeneous data to model and discover properties of biological systems. A main goal of the Laboratory of Systems and Synthetic Biology is to gain a systems understanding of societal relevant microorganisms and microbial ecosystems and to translate this knowledge into applications of biotechnological, medical and environmental interest.


Microbial Bioengineering uses knowledge-based bioengineering to re-design and modify microbial systems for biotechnological applications. We develop and apply novel technologies to advance the development of microbial cell factories. Key components of this approach are the use of genome scale metabolic models and integrated genomics approaches for bioengineering target identification and genome streamlining to generate simplified, stabilized and highly characterized strains as microbial chassis for innovative biotechnological applications.

The Microbial Bioengineering group has a strong expertise particularly in filamentous fungi as cell factories and as sources of industrially relevant metabolites and enzymes. Fungi form a class of relatively simple eukaryotic organisms that perform biological processes essentially based on the same principles as biological processes in higher eukaryotes. As microbial cell factories they have very desirable characteristics, namely a high level of protein secretion, metabolite production and metabolic versatility. For these reasons, they are being increasingly used for the large-scale production of enzymes and a wide-range of (semi-)bulk chemicals and pharmaceuticals.


For details see projects.

Recent Publications

J Sloothaak, DI Odoni, LH de Graaff, VAP Martins dos Santos, PJ Schaap, JA Tamayo-Ramos (2015) Aspergillus niger membrane-associated proteome analysis for the identification of glucose transporters. Biotechnology for biofuels 8 (1), 1

Ruud Heshof, Leo H de Graaff, Juan J Villaverde, Armando JD Silvestre, Thomas Haarmann, Trine K Dalsgaard, Johanna Buchert (2015) Industrial potential of lipoxygenases. Critical reviews in biotechnology 1-10       

L van der Straat, LH de Graaff (2014) Pathway transfer in fungi: Transporters are the key to success. Bioengineered 5 (5), 335-339

A full list of recent publications by can be found here.

Microbial Systems Biology 1