Thomas (Tom) H.A. Ederveen, PhD

I'm a senior scientist at the Radboudumc Nijmegen, currently active in the Bacterial Genomics bioinformatics group and the Department of Dermatology. Here, we focus mainly on the analysis of genomes of bacteria, on human and animal microbiota (i.e. microbiome studies) and on bacterial strain tracking. I’m also closely involved at NIZO health and food research (Ede) for one day a week as a guest employee, in order to maintain fruitful collaborations between Radboudumc and NIZO in the dynamic field of microbiota and health.

I see myself as a biologist applying public bioinformatics tools and approaches in order to make sense out of microbial samples from various biological sources (*), in the field of (medical) biology and food and nutrition. Much of my own work relates to the analysis of the human microbiome in both healthy and disease status, in order to identify desirable and undesirable bacteria respectively. In the end, by understanding these processes we hope to come up with interventions to cure diseases underlying an imbalance (dysbiosis) in the human microbiome.


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Curriculum Vitae (CV) Thomas (Tom) H.A. Ederveen   Dissertation (PhD) Thomas (Tom) H.A. Ederveen


* Expertise and Application :
The research in our team involves (meta)genome sequencing (WGS / Shotgun), metataxonomics (16S / ITS), multi- and single-locus sequence typing (MLST / SLST), transcriptomics, bacterial genome assembly and annotation, gene-trait matching and comparative genomics, among others; and with specific focus on samples from humans (e.g. skin, oral or gut microbiome), but also from animals, the environment (e.g. soil or plants) or food (e.g. cheese or related fermentation products).

Image of Thomas (Tom) H.A. Ederveen

Publications

# 2019
Smits J.P.H., Ederveen T.H.A., Rikken G., van den Brink N.J.M., van Vlijmen-Willems I.M.J.J., Boekhorst J., Kamsteeg M., Schalkwijk J., van Hijum S.A.F.T., Zeeuwen P.L.J.M., van den Bogaard E.H., TARgeting the cutaneous microbiota in atopic dermatitis by coal tar via AHR-dependent induction of antimicrobial peptides. J Invest Dermatol, Jul;[Epub Ahead of Print]

Gommers L.M.M., Ederveen T.H.A., van der Wijst J., Overmars-Bos C., Kortman G.A.M., Boekhorst J., Bindels R.J.M., de Baaij J.H.F., Hoenderop J.G.J., Low gut microbiota diversity and dietary magnesium intake are associated with the development of PPI-induced hypomagnesemia. FASEB J, Jul;[Epub Ahead of Print]

Link to Open Access Location Rogier R., Ederveen T.H.A., Wopereis H., Hartog A., Boekhorst J., van Hijum S.A.F.T., Knol J., Garssen J., Walgreen B., Helsen M.M., van der Kraan P.M., van Lent P.L.E.M., van de Loo F.A.J., Abdollahi-Roodsaz S., Koenders M.I., Supplementation of diet with non-digestible oligosaccharides alters the intestinal microbiota, but not arthritis development, in IL-1 receptor antagonist deficient mice. PLoS One, Jul;14(7):e0219366

Link to Open Access Location Chermprapai S., Ederveen T.H.A., Broere F., Broens E.M., Schlotter Y.M., van Schalkwijk S., Boekhorst J., van Hijum S.A.F.T., Rutten V.P.M.G., The bacterial and fungal microbiome of the skin of healthy dogs and dogs with atopic dermatitis and the impact of topical antimicrobial therapy, an exploratory study. Vet Microbiol, Feb;229:90-99

# 2018
Link to Open Access Location Ederveen T.H.A.*, Ferwerda G.*, Ahout I.M., Vissers M., de Groot R., Boekhorst J., Timmerman H.M., Huynen M.A., van Hijum S.A.F.T.*, de Jonge M.I.*, Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses. Microbiome, Jan;6(1):10

# 2017
Link to Open Access Location Aarts E.*, Ederveen T.H.A.*, Naaijen J., Zwiers M.P., Boekhorst J., Timmerman H.M., Smeekens S.P., Netea M.G., Buitelaar J.K., Franke B., van Hijum S.A.F.T.*, Arias Vasquez A.*, Gut microbiome in ADHD and its relation to neural reward anticipation. PLoS One, Sep;12(9):e0183509

Link to Open Access Location Rogier R.*, Ederveen T.H.A.*, Boekhorst J., Wopereis H., Scher J.U., Manasson J., Frambach S.J.C.M., Knol J., Garssen J., van der Kraan P.M., Koenders M.I., van den Berg W.B., van Hijum S.A.F.T., Abdollahi-Roodsaz S., Aberrant intestinal microbiota due to IL-1 receptor antagonist deficiency promotes IL-17- and TLR4-dependent arthritis. Microbiome, Jun;5(1):63

Link to Open Access Location Zeeuwen P.L., Boekhorst J., Ederveen T.H.A., Kleerebezem M., Schalkwijk J., van Hijum S.A.F.T., Timmerman H.M., Reply to Meisel et al. : Skin microbiome surveys are strongly influenced by experimental design. J Invest Dermatol, Apr;137(4):961-962

Link to Open Access Location Zeeuwen P.L.*, Ederveen T.H.A.*, van der Krieken D.A.*, Niehues H.*, Boekhorst J., Kezic S., Hanssen D.A., Otero M.E., van Vlijmen-Willems I.M., Rodijk-Olthuis D., Falcone D., van den Bogaard E.H., Kamsteeg M., de Koning H.D., Zeeuwen-Franssen M.E., van Steensel M.A., Kleerebezem M., Timmerman H.M., van Hijum S.A.F.T., Schalkwijk J., Gram-Positive Anaerobe Cocci (GPAC) are Underrepresented in the Microbiome of Filaggrin-Deficient Human Skin. J Allergy Clin Immunol, Apr;139(4):1368-1371

# 2016
Link to Open Access Location van der Krieken D.A.*, Ederveen T.H.A.*, van Hijum S.A.F.T., Jansen P.A., Melchers W.J., Scheepers P.T., Schalkwijk J., Zeeuwen P.L.,
An In vitro Model for Bacterial Growth on Human Stratum Corneum.
Acta Derm Venereol, Nov;96(7):873-879

# 2013
Link to Open Access Location Ederveen T.H.A., Overmars L., van Hijum S.A.F.T., Reduce Manual Curation by Combining Gene Predictions from Multiple Annotation Engines, a Case Study of Start Codon Prediction. PLoS One, May;8(5):e63523

# 2011
Ederveen T.H.A., Mandemaker I.K., Logie C., The Human Histone H3 Complement Anno 2011. Biochim Biophys Acta, Oct;1809(10):577-86



Dissertation (PhD)

# 2019
Link to Open Access Location Ederveen T.H.A., Co-Promoters: van Hijum S.A.F.T., Boekhorst J., Zeeuwen P.L., Promotor: Schalkwijk J., On the role of host microbiota associated with health and disease - a metagenomics survey through marker-gene sequencing and genomics approaches. Radboud University, Nijmegen, March 28, 2019

Software

Bioinformatics Tools and Software:

COMPANION   for Comparative Genome Annotation   ( Ederveen et al., PLoS One, 2013 )
TaxPhlAn   for Taxonomy Phylogenetic Analysis   ( Ederveen et al., in preparation, 2019 )



DockerHub   GitHub

Contact

Click here for my Radboudumc webpage.


E-mail address:

Tom [dot] Ederveen [at] radboudumc.nl

Visiting address:

Radboud University Medical Center
CMBI department (room 0.08)
RIMLS Research Tower (ground floor)
Geert Grooteplein Zuid 28, route 260
6525 GA, Nijmegen, The Netherlands

Phone number:

+31 (0)24 36 19390 (office)