Thomas Ederveen

Thomas Ederveen
Radboud University Medical Centre (Radboudumc) · CMBI (bioinformatics) Department, group of Bacterial Genomics

Doctor of Philosophy

About

19
Publications
3,075
Reads
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507
Citations
Introduction
I'm a senior scientist at the Radboudumc Nijmegen, currently active in the Bacterial Genomics bioinformatics group and 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 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.
Additional affiliations
October 2012 - present
Radboud University Medical Centre (Radboudumc)
Position
  • Researcher
Education
March 2014 - February 2019
Radboud University
Field of study
September 2009 - July 2012
Radboud University
Field of study
  • Medical Biology

Publications

Publications (19)
Article
Full-text available
Mutations in the filaggrin gene, which cause the skin disease ichthyosis vulgaris and are a genetic risk factor for atopic dermatitis, alter the cutaneous microbiome thereby affecting keratinocyte host defense responses following skin barrier disruption.
Article
Full-text available
Background Microorganisms in the human intestine (i.e. the gut microbiome) have an increasingly recognized impact on human health, including brain functioning. Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental disorder associated with abnormalities in dopamine neurotransmission and deficits in reward processing and its underly...
Article
Full-text available
Background: Perturbation of commensal intestinal microbiota has been associated with several autoimmune diseases. Mice deficient in interleukin-1 receptor antagonist (Il1rn-/-mice) spontaneously develop autoimmune arthritis and are susceptible to other autoimmune diseases such as psoriasis, diabetes, and encephalomyelitis; however, the mechanisms...
Article
Full-text available
Canine atopic dermatitis is a genetically predisposed inflammatory and pruritic allergic skin disease that is often complicated by (secondary) bacterial and fungal (yeast) infections. High-throughput DNA sequencing was used to characterize the composition of the microbiome (bacteria and fungi) inhabiting specific sites of skin in healthy dogs and d...
Article
Full-text available
Background While almost all infants are infected with respiratory syncytial virus (RSV) before the age of 2 years, only a small percentage develops severe disease. Previous studies suggest that the nasopharyngeal microbiome affects disease development. We therefore studied the effect of the nasopharyngeal microbiome on viral load and mucosal cytoki...
Article
Full-text available
Background The cervicovaginal microbiome (CVM) plays a significant role in women’s cervical health and disease. Microbial alterations at the species level and characteristic community state types (CST) have been associated with acquisition and persistence of high-risk human papillomavirus (hrHPV) infections that may result in progression of cervica...
Article
Maternal gestational obesity is a risk factor for offspring’s neurodevelopment and later neuro-cognitive disorders. Altered gut microbiota composition has been found in patients with neurocognitive disorders, and in relation to maternal metabolic health. We explored the associations between gut microbiota and cognitive development during infancy, a...
Article
Late cornified envelope (LCE) proteins are predominantly expressed in the skin and other cornified epithelia. Based on sequence similarity, this eighteen-member homologous gene family has been subdivided into six groups. The LCE3 proteins have been the focus of dermatological research, as the combined deletion of LCE3B and LCE3C genes (LCE3B/C-del)...
Article
Full-text available
Background Hand eczema is a common inflammatory skin condition of the hands whose pathogenesis is largely unknown. More insight and knowledge of the disease on a more fundamental level might lead to a better understanding of the biological processes involved, which could provide possible new treatment strategies. We aimed to profile the transcripto...
Article
Full-text available
Microbiota live in a closely regulated interaction with their environment, and vice versa. The presence and absence of microbial entities is greatly influenced by features of the niche in which they thrive. Characteristic of this phenomenon is that different human skin sites harbor niche‐specific communities of microbes. Microbial diversity is cons...
Article
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We present TaxPhlAn, a new method and bioinformatics pipeline for design and analysis of single-locus sequence typing (SLST) markers to type and profile bacteria beyond the species-level in a complex microbial community background. TaxPhlAn can be applied to any group of phylogenetically-related bacteria, provided reference genomes are available. A...
Article
Proton pump inhibitors (PPIs) are used by millions of patients for the treatment of stomach acid-reflux diseases. Although PPIs are generally considered safe, about 13% of the users develop hypomagnesemia. Despite rising attention for this issue, the underlying mechanism is still unknown. Here, we examine whether the gut microbiome is involved in t...
Article
Full-text available
The intestinal microbiome is perturbed in patients with new-onset and chronic autoimmune inflammatory arthritis. Recent studies in mouse models suggest that development and progression of autoimmune arthritis is highly affected by the intestinal microbiome. This makes modulation of the intestinal microbiota an interesting novel approach to suppress...
Article
Skin colonization by Staphylococcus aureus and its relative abundance is associated with atopic dermatitis (AD) disease severity and treatment response. Low levels of antimicrobial peptides in AD skin may be related to the microbial dysbiosis. Therapeutic targeting of the skin microbiome and antimicrobial peptide expression can, therefore, restore...
Article
The diversity and dynamics of the skin microbiome in health and disease have been studied recently, but adequate model systems to study skin microbiotas in vitro are largely lacking. We developed an in vitro system that mimics human stratum corneum, using human callus as substrate and nutrient source for bacterial growth. The growth of several comm...
Article
Full-text available
Nowadays, prokaryotic genomes are sequenced faster than the capacity to manually curate gene annotations. Automated genome annotation engines provide users a straight-forward and complete solution for predicting ORF coordinates and function. For many labs, the use of AGEs is therefore essential to decrease the time necessary for annotating a given...
Article
Full-text available
Histones are highly basic, relatively small proteins that complex with DNA to form higher order structures that underlie chromosome topology. Of the four core histones H2A, H2B, H3 and H4, it is H3 that is most heavily modified at the post-translational level. The human genome harbours 16 annotated bona fide histone H3 genes which code for four H3...

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