Dr. ir. Frederiek-Maarten Kerckhof

Telephone number: 
+32 9/264 59 80
Visiting scientists

Background information


  • 2006-2011 M.Sc. Bioscience engineering option cellular & genetic biotechnology major computational biology
  • M.Sc. thesis: Unconventional electron donors and acceptors for microbial ecosystems - expertise in Bio-electrochemical systems (BES) - Laboratory of Microbial Ecology and Technology (LabMET), Ghent University
  • M.Sc. project bio-informatics & statistics for genome analysis: Antarctic metagenomics - pyrosequencing analysis pipeline
  • B.Sc. thesis: Competition and diversity: opposites or partners?
  • 2011-2016 Ph. D.: Doctor in Applied Biological Sciences, Doctoral School of Bioscience Engineering, Ghent University
  • 2016-2017 IAP network project coordinator "Microbial Resource Managment" (P7/25) www.mrm.ugent.be
  • 2018-2019 IOF StepStone postdoc (www.kytos.be)
  • 2019-2021 VLAIO Spin-off IM Postdoc (www.kytos.be)

Research interests: 

  • Mixed microbial community ecology
  • Next generation sequencing and analysis of metagenomics data
  • Statistics in microbial ecology
  • Methanotrophic ecology

Specific research topics

Sustainable methanotrophs

In August, 2011 I got the amazing oportunity to work at CMET just one year after graduating as a master in Bioscience engineering - option cellular & genetic biotechnology with a major in computational biology. Apart from a solid background in machine learning, unsupervised learning & statistics and general modelling and bioinformatics programming I have a very profound interest in microbial ecology. I believe that the nexus of computational biology and computational techniques will be at the source of renewed insight and applications in microbial ecology.

My PhD research focussed on fluxes through methanotrophic consortia and is funded by a GOA from Ghent University. In a first work package, I experimented with several environmental stresses on mixed methanotrophic communities in order to accumulate valuable compounds from waste streams containing methane (e.g. biogas, syngas, ...). In the next workpackages I focused on ecosystems networking and optimization of methanotrophic associations. Using stable isotope probing I am investigating the carbon fluxes through methanotrophic communities, which I validated by means of synthetic ecology approaches.

As of August, 2016 I am working as the coordinating post-doc of an inter-university attraction poles network (IAP) on microbial resource managment. Specifically, in this network we evaluate the applications of synthetic ecosystems to unravel microbial ecological processes in nature.

Bio-informatics and statistics

As a key player of the biostatistics and bio-informatics group of CMET I am involved in several projects among which I am investigating multiple microbiomes with my in-house developed mothur- and R-based pipeline for next-generation data analysis, visualization and statistics.

Selected key publications: 
Kerckhof, Frederiek-Maarten, et al. "Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity." PloS one 9.6 (2014).
Props, R., Kerckhof, F. M., Rubbens, P., De Vrieze, J., Sanabria, E. H., Waegeman, W., ... & Boon, N. (2017). Absolute quantification of microbial taxon abundances. The ISME journal, 11(2), 584-587.
Buysschaert, B., Kerckhof, F. M., Vandamme, P., De Baets, B., & Boon, N. (2018). Flow cytometric fingerprinting for microbial strain discrimination and physiological characterization. Cytometry Part A, 93(2), 201-212.
Acosta, N., Sakarika, M., Kerckhof, F. M., Law, C. K. Y., De Vrieze, J., & Rabaey, K. (2019). Microbial protein production from methane via electrochemical biogas upgrading. Chemical Engineering Journal, 123625.