Microbial Genomics & Microbiomics
Microbial Genomics & Microbiomics
The Microbial Genomic & Microbiomics research group - under leadership of prof. dr. Rob Willems (who succeeded prof. dr. Marc Bonten as group leader as of 2017) - has three major research lines: (1) Molecular & Cellular Host-Microbiota Interactions, (2) Microbiomics and (3) Genomics & Genome-based Epidemiology of Antimicrobial Resistance.
Research interests / topics uitklapper, klik om te openen
Molecular & Cellular Host-Microbiota Interactions
PI: Dr. Marcel de Zoete, associate professor
The intestinal microbiota plays a key role in health and disease, often through direct bacterial interactions with the host intestinal (immune) cells or by released bacterial metabolites. Our main goal is to understand molecular mechanisms that underly pathogenic host-microbiota interactions. An important focus are ‘pathogenic’ commensals called pathobionts, which often live within the intestinal mucus layer in close proximity or attached to intestinal epithelial cells. The interactions of these pathobionts with the host epithelium and immune system are mostly unclear but believed to dramatically impact on various disease, including inflammatory bowel disease, colorectal cancer and metabolic syndrome. By unraveling the molecular mechanisms behind pathological host-microbiota interactions, we aim to pave the road for the development of novel therapeutic approaches.
More about Molecular & Cellular Host-Microbiota Interactions
Microbiomics
PI: Dr. Fernanda Paganelli, assistant professor
We use next generation sequencing techniques to determine the role of the microbiome in relation to disease, such as chronic infectious and immunological diseases as well as transmission of antibiotic resistant genes in communities and hospitals. Furthermore, we use colon organoids model to study the host response to specific bacterial communities.
Genomics & Genome-based Epidemiology of Antimicrobial Resistance
PI: Dr. Anita Schürch, assistant professor
Dissemination of physiologically important traits encoded on plasmids, integrons, transposons, and bacteriophages are highly dynamic because these mobile genetic elements (MGE) transmit with ease. The most prominent example is the spread of antimicrobial resistance (AMR) genes through different hosts and environments. We develop novel computational methods to reconstruct plasmids and other MGEs and to map their dissemination. Several genomics software tools have been developed and made made publicly available by this research group, including Gplas and mlplasmids.
More about Genomics & Genome-based Epidemiology of Antimicrobial Resistance
About the group leader(s) uitklapper, klik om te openen
Prof. dr. Rob Willems studied biology at the Free University in Amsterdam and acquired his PhD from the Utrecht University in 1993 on “Genetic and functional studies on Bordetella pertussis fimbriae”. After postdoc positions at the Faculty of Veterinary Medicine, Utrecht University and at the Department of Infectious Diseases of the University Hospital, Leiden he became research scientist and section head at the National Institute for Public Health and the Environment (RIVM) in 1996. In 2003 he moved from the RIVM to the University Medical Center Utrecht where he became assistant professor. In 2008 he was appointed associate professor and since December 1st 2016, he is full professor of Population Genetics of Antibiotic Resistance at the department of Medical Microbiology of the University Medical Center Utrecht.
Group members
Assistant professor:
Dr. Janetta Top
Postdocs:
Dr. Victoria Pascal
PhD candidates and their research projects:
Guus van Muijlwijk
Jiannan Cui
Coco Duizer
Jesse Kerkvliet - "Gene flow networks in animals, the food chain and the environment"
Paul Stege - "Molecular mechanisms of microbiota-mediated colonization resistance against intestinal outgrowth of multidrug-resistant Enterobacteriaceae (E. coli, K. pneumoniae) and enterococci"
Roos Berbers
Jery Baan
Julian Paganini - "Population genomics of antibiotic-resistant E. coli and potential plasmid transmission in ICU patients"
Matteo Buffoni - "Mobile Genetic Elements involved in Antimicrobial Resistance"
Rick Verheijden
Bioinformaticians:
Malbert Rogers
Rodrigo Silva Meneses
Research technicians:
Marco Viveen
Iris Braat
Jelle Scharringa
Moniek Salomons
Education / Courses uitklapper, klik om te openen
- Research Programme Infection and Immunity, Graduate School of Life Sciences, Utrecht University
- Infection Meets Immunity Summer School, Infection & Immunity PhD program, Utrecht University
Achievements
Funding & Grants
Collaborations uitklapper, klik om te openen
UMC Utrecht (Netherlands)
Prof. dr. Jeffrey Beekman, Department of Pediatrics, Wilhelmina Children's Hospital
Prof. dr. Onno Kranenburg, Laboratory for Translational Oncology, dLAB
Prof. dr. Jurgen Kuball, Center for Translational Immunology, dLAB
Dr. Caroline Lindemans, Department of Pediatrics, Wilhelmina Children's Hospital
Prof. dr. Linde Meyaard, Center for Translational Immunology, dLab
Prof. dr. Bas Oldenburg, Department of Gastroenterology and Hepatology, dIGD
Prof. dr. Janneke van de Wijgert, Research Program Infectious Diseases, Julius Center
Prof. dr. Femke van Wijk, Center for Translational Immunology, dLAB
Dr. Noortje Ijssennagger, Center for Molecular Medicine, dLAB
Dr. Marjolein de Bruin-Weller, Department of Dermatology and Allergology, dIGD
Dr. Helen Leavis, Department of Rheumatology & Clinical Immunology, dIGD
Dr. Gaby Steba, Department of Reproductive Medicine and Gynaecology, dV&B
Dr. Karijn Suijkerbuijk, Department of Medical Oncology, Cancer Center
Dr. Hae-Won Uh, Department of Biostatistics and Research Support, Julius Center
Dr. Lilly Verhagen, Department of Infectious diseases and Immunology, Wilhelmina Children's Hospital
Utrecht University (Netherlands)
Prof. dr. Jos van Putten, Institute of Veterinary Sciences, Faculty of Veterinary Medicine
Dr. Aldert Zomer, PhD, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine
Dr. Bas Dutilh, Theoretical Biology & Bioinformatics, Faculty of Sciences
Dr. ing. Tom Wennekes, Department of Pharmaceutical Sciences, Faculty of Sciences
Dr. Karin Strijbis, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine
Exeter University, Exeter (Great Britain)
Dr. Stineke van Houte, Department of Biosciences
Yale University, New Haven CT (USA)
Dr. Noah Palm, Department of Immunobiology
Hasbro Children's Hospital, Providence RI (USA)
Dr. Jason Shapiro, Department of Pediatric Gastroenterology
In the media uitklapper, klik om te openen
- August 16, 2019 - www.nationalezorggids.nl - Fernanda Paganelli
Maagverkleining verandert de samenstelling van de darmflora
Contact information
Prof. dr. R.J.L. (Rob) Willems
Department of Medical Microbiology
G04.609
UMC Utrecht
The Netherlands