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Department of Microbiology and Systems Biology TNO

Contact Details


Utrechtseweg 48, 3704HE, Zeist


dr. J. Bouwman

0031 (0)6 11700518

Hotel Description

TNO is internationally acclaimed for finding innovative solutions for diverse challenges in to reduce the burden of lifestyle-related diseases, such as Type 2 Diabetes and obesity and their complications. Related to the objectives of DTL, TNO applies dedicated expertise in data generation, data basing infrastructure, statistics, machine learning, and network biology to proficiency in systems biology of health and (metabolic ) disease. We combine a broad collection of state-of-the-art analytical platforms (e.g. NanoString Technologies, microbial sequencing, targeted metabolomics platforms  and protein biomarker analysis) and in silico approaches with an extensive collection of in vitro and in vivo models of health and disease.  


Our key technical capabilities (related to DTL objectives) are: 
Human and pre-clinical studies for nutrition and pharma applications: from study design to data analyses and biological interpretation; 

• Metabolomics platforms (e.g. short chain fatty acids, amino acids,  bile acids) including biological interpretation; 

Targeted gene expression analysis with NanoString platform, bioinformatics and biological interpretation. The gene panels vary from proprietary fibrosis or Fibrosis+ panels to pre-defined NanoString panels (commercially available). 

Targeted protein biomarkers with MSD and ELISA with special focus on optimization of assays to achieve accurate and robust analyses in low sample volumes (relevant for cohorts where sample volumes are limited). 

• Microbiome analysis, including amplicon sequencing, bioinformatic analysis and FAIR data management of metagenomic data (leading the JPI INTIMIC knowledge platform). Expertise focus on metabolic and respiratory disease  

• Data warehousing for (pre)clinical omics, phenotypic studies and n=1 studies 

• FAIR Data warehousing for nutrition and prevention 

• Distributed learning, Multi-party computation and machine learning 

• Complex statistical analysis of heterogeneous datasets; 

• Network biology, mechanistic interpretation and prioritization of cross-omics data; 


Systems biology
  • Agri & Food
  • Biomedical & health
  • Mechanism of action investigations (particularly in Type-2 Diabetes, CVD, OA, fibrosis): analysis of nutritional effect, pharmaceutical drug effects, disease etiology elucidation, identification of novel candidate drug targets
  • Discovery, prioritization and validation of diagnostic, prognostic, and predictive biomarkers for assessment of: efficacy, safety, patient stratification, on risk and responders, patient motivation, predictive toxicology
  • Metabolomics analytical platforms with specialities such as endocannabinoids, bile acids, eicosanoids: analysis of microbiome composition, drug repurposing, repositioning
  • Metabolic health and disease
  • Systems toxicology
  • Nutrigenomics
  • Biotechnology
  • Microbiology

Expertise and Track Record

43500985044 Novel sequencing methods for skin microbiome in relation to atopic dermatitis with S. Pasmans (Erasmus MC).

We offer state of the art technology, highly educated personnel in many areas combined with excellent project management. We are very strong in designing tailor-made projects to solve specific research questions from the industry.

• Netherlands Metabolomics centre
o Consultancy on interpretation of metabolomics data in at least 8 NMC projects
o Given support on the usage of the Phenotype database
• EU project NU-AGE
• EU project EURRECA
o EU projects:  NU-AGE, Cartardis, EURRECA, MyNewGut, ENPADASI, JPI INTIMIC knowledge platform

• Participation in >30 EU FP6, FP7 and H2020 projects as RTD, as coordinator or work package leader. We are valued because of our professional project focus, experience in translating findings to clinical, commercial applications, our expertise in data handling and biological network analysis, and our biological and mechanistic knowledge.  

  • Pellis L, van Erk MJ, van Ommen B, Bakker GC, Hendriks HF, Cnubben NH, Kleemann R, van Someren EP, Bobeldijk I, Rubingh CM, Wopereis S. Plasma metabolomics and proteomics profiling after a postprandial challenge reveal subtle diet effects on human metabolic status. Metabolomics. 2012 Apr;8(2):347-359
  • Bouwman J, Vogels JT, Wopereis S, Rubingh CM, Bijlsma S, Ommen Bv., Visualization and identification of health space, based on personalized molecular phenotype and treatment response to relevant underlying biological processes. BMC Med Genomics. 2012
  • Van Schalkwijk DB, van Ommen B, Freidig AP, van der Greef J, de Graaf AA.Diagnostic markers based on a computational model of lipoprotein metabolism.J Clin Bioinforma. 2011 Oct 26;1(1):29
  • Crielaard W, Zaura E, Schuller AA, Huse SM, Montijn RC, Keijser BJ. Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health. BMC Med Genomics. 2011 Mar 4;4:22
  • Van der Greef J, van Wietmarschen H, van Ommen B, Verheij E (2013). Looking back into the future: 30 years of metabolomics at TNO. Mass Spectrom Rev. doi: 10.1002/mas.21370
  • Van Ommen B, El-Sohemy A,Hesketh J and 16 others -The micronutrient genomics project: creating a community driven knowledge base for micronutrient research – Genes and Nutrition, 2009, 5 (3) 189-203 DOI 10.1007/s12263-010-0192-8
  • Van Ommen B, Bouwman J and 16 others , Challenges of molecular nutrition research 6: The Nutritional Phenotype database to store, share and evaluate nutritional systems biology studies. Genes and Nutrition 5 (2010), 189- 203 - DOI 10.1007/s12263-010-0167-9
  • Ranges of phenotypic flexibility in healthy subjects. van den Broek TJ, Bakker GCM, Rubingh CM, Bijlsma S, Stroeve JHM, van Ommen B, van Erk MJ, Wopereis S. Genes Nutr. 2017 Dec 6;12:32.
  • Plasma metabolome analysis identifies distinct human metabotypes in the postprandial state with different susceptibility to weight loss-mediated metabolic improvements. Fiamoncini J, Rundle M, Gibbons H, Thomas EL, Geillinger-Kästle K, Bunzel D, Trezzi JP, Kiselova-Kaneva Y, Wopereis S, Wahrheit J, Kulling SE, Hiller K, Sonntag D, Ivanova D, van Ommen B, Frost G, Brennan L, Bell J, Daniel H. FASEB J. 2018 Oct;32(10):5447-5458.
  • Proposed guidelines to evaluate scientific validity and evidence for genotype-based dietary advice. Grimaldi KA, van Ommen B, … , Verschuren L, Virgili F, Weber P, Bouwman J. Genes Nutr. 2017 Dec 15;12:35

TNO is participant in: 
DTL – founding member, DISC CT member 
TI Coast– project partner 
NuGO organisation –Director 
NMC (Netherlands Metabolomics Centre) – Founding member, steering group member, data support platform – Principle Investigator 
NTC (Netherlands Toxicogenomics Centre) – partner 
TIFN (Top Institute Food and Nutrition) – project partner 
CTMM (Center for Translational Molecular Medicine) – project partner 
TI Pharma – project partner 

EU FP6 and FP7 – project coordinator or project partner in a variety of projects (eg EURRECA, NuGO, Bioclaims, Nutritech, Food4me, NU-AGE, CARTARDIS, MISSION-T2D, D-BOARD, MyNewGut, ENPADASI, JPI INTIMIC knowledge platform) 

EU coordination activity – project partner (eg Cosmos, EURO-DISH (via NuGO)) 
IMI – project partner 
EuropaBio Personalized Medicine Topic Group – steering committee member 

Hotel Characteristics

  • 6
  • 2
  • 3


  • servers including servers for heavy calculation work

ISO 9001

Phenotype database (www.dbnp.org)