Prof. dr. ir. Nico Boon

Telephone number: 
+32 9/264 59 76
Faculty staff


  • Master in Bio-engineer Cell and Gene Biotechnology; Ghent University; 1998
  • Ph.D. in Applied Biological Sciences; Ghent University; 2002

Professional activities

  • Head of the Department of Microbial and Biochemical Technology (Ghent University); 2011 – 2014; 2016 - 2017
  • Full Professor (Tenured; “Hoogleraar”) of Molecular Microbial Ecology (ZAP) at the Center for Microbial Ecology and Technology (Ghent University); 2014 – present
  • Associate Professor (Tenured; “Hoofddocent”) of Molecular Microbial Ecology (ZAP) at the Laboratory of Microbial Ecology and Technology (Ghent University); 2011 – 2014
  • Assistant Professor (Tenured; “Docent”) of Molecular Microbial Ecology (ZAP) at the Laboratory of Microbial Ecology and Technology (Ghent University); 2006 – 2011
  • FWO-post doc position awarded at the Laboratory of Microbial Ecology and Technology (Ghent University); 2006
  • Doctor-assistant position (AAP) at the Laboratory of Microbial Ecology and Technology (Ghent University); 2003 – 2006
  • Assistant position (AAP) at the Laboratory of Microbial Ecology and Technology (Ghent University); 2001 – 2003
  • Doctoral research at the project grant G.O.A. 12050797 of the "Ministerie van de Vlaamse Gemeenschap, Bestuur Wetenschappelijk Onderzoek" (Belgium); 1998 – 2001


Nico Boon is leading the Microbial Community Engineering (MiCE) group within the Center of Microbial Ecology and Technology (CMET) at Ghent University. Since 1998 his research is focused on the applied microbial ecology of managed and engineered ecosystems. The areas of interests have been the development of molecular methods (Next Generation Sequencing, Fluorescent in situ Hybridisation, Real-Time PCR and Flow Cytometry) for the qualitative and quantitative description of microorganisms and investigations of microbial processes in carbon and nitrogen cycling, novel bioaugmentation strategies for xenobiotics and the bioprecipitation and application of catalytic particles (Pd, Mn, Au and Ag). During the last years, the research interests are focussed on the development of new microbial ecological theories to link the microbial community structure to functionality. The central theme of this research is to understand of the composition, functionality and the limits under which a microbial community can (optimally) perform. At present, there is only limited theoretical insight in the ecology of mixed microbial cultures and engineering practices to manage those microbial resources are fragmentary. The final aim is to structure and optimize the performance of the community in respect to a desirable set of outputs. This strategy is called Microbial Resource Management (MRM).

Research Leadership

Prof. Nico Boon is currently project promoter of a major national GOA projects “Collaboromics : identifying and engineering core and satellite populations in (synthetic) microbial ecosystems” and "Biostable" (FWO-SBO). He is also scientific partner in the H2020 project ELECTRA (CE-BIOTEC-04-2018). He is also promoter or co-promoter of several national projects dealing with the microbial ecology of different environments. Previously, he was coordinator of the most important Belgian research program “Interuniversity Attraction Poles (IAP) Phase VII” of the Belgian Federal Science Policy Office (2012-2017) and coordinator of the FP7 ManureEcoMine (2013-2017). During his career, he participated as partner or WP leader in more than 10 EU projects.

Publications and presentations

(Web of Science ResearcherIDGoogle ScholarOrcidUGent - academic library)

The research has resulted in almost 540 accepted/published international publications in journals with peer review. He has been cited more than 45000 times with a h-index of 88 (WoS) or 113 (Google Scholar) and is taken up in the list of ISI Highly Cited Researchers (2018, 2019). He published in top journals, like Nature, Nature Communications, FEMS Microbiology Reviews, Trends in Biotechnology, PLoS Pathogens, Plos One (6x), Current Opinion in Biotechnology (2x), Biotechnology Advances (2x), Trends in Biotechnology (3x), ISME Journal (5x)… He has also seven patents. He (co)organized more than 30 (inter)national conferences and he gave 85 national and international oral presentations at conferences and institutions. 

Teaching and supervision

Nico Boon was the supervisor of 63 finished PhD’s and is currently supervising 20 Ph.D.-students in microbial ecology and environmental engineering, and he has supervised more than 150 master students at Ghent University. He had within his group 23 postdocs at a junior or senior level. 
He coordinates several courses at the Bachelors and Masters level: Microbial Ecological Processes (since 2006), Molecular Microbial Techniques (2006-2014; 2016-2019), Microbiomics (since 2020) and Environmental Microbiology (since 2011). At the faculty of Bioscience Engineering, he was the coordinator of the Master Bio-engineer Cell and Gene Biotechnology and was responsible for the restructuring of the Masters program (2009-2014). He has organized or co-organized more than 30 national and international workshops

Selected key publications: 
Wittebolle, L., M. Marzorati, L. Clement, A. Balloi, D. Daffonchio, K. Heylen, P. De Vos, W. Verstraete, and N. Boon. 2009. Initial community evenness favors functionality under selective stress. Nature 458:623-626.
De Roy, K., M. Marzorati, A. Negroni, O. Thas, A. Balloi, F. Fava, W. Verstraete, D. Daffonchio, and N. Boon. 2013. Invasion preserves functionality in uneven stressed communities. Nature Communications 4:1383
De Roy, K., L. Clement, O. Thas, Y. Y. Wang, and N. Boon. 2012. Flow cytometry for fast microbial community fingerprinting. Water Research 46:907-919.
Wang, Y., F. Hammes, K. De Roy, W. Verstraete, and N. Boon. 2010. Past, present and future applications of flow cytometry in aquatic microbiology. Trends in Biotechnology 28:416-424.
Boon, N., W. De Windt, W. Verstraete, and E. M. Top. 2002. Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiology Ecology 39:101-112.