Advancing Functional Metagenomics using Synthetic Biology from Soil to Sequence

Eric van der Helm

Research output: Book/ReportPh.D. thesisResearch


Facing a growing and aging world population, mankind is in need for new drug molecules and ways to produce nutrients. Instead of using chemical synthesis, drugs and nutrients can be produced in a sustainable way by modified bacteria.Most of those interesting molecules are already produced by billions of bacteria in the environment. Unfortunately it is difficult to grow the majority of the bacteria in a laboratory and it is therefore not possible to use their capabilities directly. However,bacteria store the information on how to produce molecules in their DNA. Using a method known as ‘functional metagenomics’, the DNA of these bacteria can be recovered from the environment and used by host-bacteria which can be grown in a lab. This allows us to make use of the capabilities of the billions of bacteria that a represent in the environment without actually growing them but by making use of their DNA instead.In my thesis I describe methods to find DNA fragments in the environment that are of interest for the biotech industry. We found for example DNA fragments in cow manure that can enhance the production of the nutrient lysine. I also describe a method to discover potential anti-viral molecules by making use of DNA from microorganisms found in soil. In this thesis I describe the application of the relatively new nanopore sequencing technology to read the DNA, which was obtained using theprevious mentioned methods. Our deFUME webserver makes it easier for researchers to investigate the DNA afterwards.
Original languageEnglish
Place of PublicationHørsholm
PublisherNovo Nordisk Foundation Center for Biosustainability
Number of pages340
Publication statusPublished - 2016


Mixed Community Bioactives

van der Helm, E., Sommer, M. O. A., Gram, L., Nørholm, M., Kortemme, T. & de Lorenzo, V.

Marie Skłodowska-Curie actions


Project: PhD

Cite this

van der Helm, E. (2016). Advancing Functional Metagenomics using Synthetic Biology from Soil to Sequence. Novo Nordisk Foundation Center for Biosustainability.