Marnix Medema

Marnix Medema

Marnix Medema
Microbial Genomics and Bioinformatics Research Group
Max Planck Institute for Marine Microbiology
Bremen, Germany

Young Investigator Award 2014

Marnix Medema is the winner of the NBIC Young Investigator Award 2014. The award ceremony is planned on April 8th from 17:30 - 18:00. The ceremony will be followed by an honorary lecture of 20 minutes.


Marinus Hendrik (Marnix) Medema was born on January 24th, 1986, in Vaassen, the Netherlands. After obtaining his B.Sc. in Biology cum laude at the Radboud University Nijmegen in 2006, he moved to Groningen to participate in the Top Master Programme in Biomolecular Sciences at the University of Groningen. He obtained his M.Sc. degree cum laude in 2008. From August 2009 to July 2013, he performed his PhD research at the University of Groningen under the supervision of Prof. Dr. Eriko Takano and Prof. Dr. Rainer Breitling, with a project on the genome mining and synthetic biology implementation of secondary metabolite biosynthetic gene clusters from microbes. During this period, he spent five months at the group of Dr. Michael Fischbach at the University of California, San Francisco. In September 2013, he obtained his doctorate with the distinction cum laude. Since August 2013, Marnix is working as a postdoctoral researcher at the group of Prof. Frank Oliver Glöckner at the Max Planck Institute for Marine Microbiology in Bremen, supported by a Rubicon grant from the Dutch Science Foundation NWO.


Title: Medicines from Microbes: exploiting the power of computational genomics for natural products discovery and engineering

Microbial secondary metabolism is a rich source of bioactive compounds with potential pharmaceutical applications. Due to the rapid acceleration of genome sequencing, computational methods have become more and more important to exploit this potential. Three major challenges can be tackled using computational genomics.

Firstly, it allows the systematic identification and classification of the gene clusters that encode compound biosynthetic routes. To this end, we constructed antiSMASH, a pipeline that automatically integrates gene cluster identification, chemical structure predictions, domain analysis of modular enzymes, and alignments between homologous gene clusters. Combining antiSMASH with a more generic algorithm, we then performed a global quantitative and comparative analysis of biosynthetic gene clusters in all microbes, the results of which lead to the identification of a major new family of secondary metabolites with >1,000 gene clusters that occur throughout many bacterial genera.

Secondly, it plays a key role in empowering the high-throughput identification of novel compounds. To make this possible for bioactive peptides, which comprise key classes of bioactive compounds, we introduce an ‘automated peptidogenomics’ method: this allows rapid computational matching of patterns in tandem mass spectrometry data to corresponding biosynthetic gene clusters in genome sequences. Even for uncultured and unsequenced strains, new molecules can thus be effectively identified and linked to their biosynthetic routes.
Thirdly and finally, computational approaches are of key importance in efforts to engineer biosynthetic gene clusters and pathways. We have devised several synthetic biology strategies to screen identified gene clusters for promising compounds and engineer their biosynthetic pathways for industry-scale production.

When combined with solid experiments, these bioinformatic approaches from various angles together have great promise to exploit the great riches of metabolism produced by microbes for the greater good of humanity.

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