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.

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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.

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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

prof. dr. R.J.L. (Rob) Willems

Full Professor

dr. A.C. (Anita) Schürch

Research Staff Other

dr. M.R. (Marcel) de Zoete

Associate Professor

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 

Related websites uitklapper, klik om te openen

Key publications

Achievements

Funding & Grants

2020 - ZonMw-ABR - €250.000

“VRE-Crosswords, horizontal or vertical? Transmission of vancomycin-resistant Enterococcus faecium in Dutch hospitals (Applicant: dr. Anita Schürch)

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2020 - Health~Holland - €1.000.000

DiSSeMINATE - Drivers of Selection and Spread of Mobile Genetic Elements Involved in antimicrobial resistance (Applicant: dr. Anita Schürch).

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2019 - Netherlands Center for One Health (NCOH) - €250.000

NCOH PhD programme ‘Complex Systems’ - Gene flow networks in animals, the food chain and the environment (Applicants: prof. dr. Rob Willems & dr. Anita Schürch).

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2019 - Janssen - €207.000

VAC52416BAC0008

2019 - Janssen - €250.000

 VAC52416BAC0001

2018 - Janssen - €1.028.000

63871860BAC0006

2018 - University of Helsinki - €90.000

2018 - One Health EJP - €39.000

MedVetKlebs JRP: Klebsiella pneumoniae: from ecology to source attribution and transmission control

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2017 - Netherlands Centre for One Health - €250.000

Metagenomics: Molecular mechanisms of microbiota-mediated colonization resistance against intestinal outgrowth of multidrug-resistant Enterobacteriaceae (E. coli, K. pneumoniae) and enterococci

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2016 - Horizon 2020 - JPI-EC-AMR JTC - €1,919.000

Selection and Transmission of Antimicrobial Resistance in Complex Systems (STARCS)

2015 - Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) - €800.000

Vidi grant for dr. Marcel de Zoete

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2014 - University of Helsinki - €225.000

Whole genome sequencing of Enterococcus faecium

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Alumni / PhD theses

Dr. Axel Janssen

2020 | Mechanisms and evolution of colistin resistance in gram-negative bacteria

Axel Janssen (1991, Nijmegen) defended his PhD thesis on November 4, 2020 at Utrecht University. The title of his thesis was “Mechanisms and evolution of colistin resistance in clinical Enterobacteriaceae”. Supervisors were prof. dr. Rob Willems and prof. dr. ir. Willem van Schaik (Department of Medical Microbiology, UMC Utrecht).

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Dr. Sergio Arredondo Alonso

2020 | Novel computational approaches to predict and reconstruct bacterial plasmids

Sergio Arredondo Alonso (1993, Barcelona) received his PhD on September 21, 2020 at Utrecht University. The title of his thesis was “Novel computational approaches to predict and reconstruct bacterial plasmids”. Supervisor was prof. dr. Rob Willems and co-supervisor was dr. Anita Schürch (both Department of Medical Microbiology, UMC Utrecht).

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Ana Maria Guzmann Prieto

2017 | Elucidating the success of Enterococcus faecium as a nosocomial pathogen through functional genomics

Ana Maria Guzman Prieto (1982, Santiago de Cali, Colombia) received her PhD on May 23, 2017 at Utrecht University. The title of her thesis was “Elucidating the success of Enterococcus faecium as a nosocomial pathogen through functional genomics”. Supervisors were prof. dr. Rob Willems, prof. dr. Marc Bonten and prof. dr. Willem van Schaijk (all Department of Medical Microbiology, UMC Utrecht).

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Elena Buelow

2015 | The human gut microbiota as a reservoir for antimicrobial resistance genes

Elena Buelow (1982, Kevelaer, Germany) received her PhD on March 24, 2015 at Utrecht University. The title of her thesis was “The human gut microbiota as a reservoir for antimicrobial resistance genes”. Supervisor was prof. dr. Marc Bonten snd co-supervisors were prof. dr. Rob Willems and prof. dr. Willem van Schaijk (all Department of Medical Microbiology, UMC Utrecht).

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Fernanda Paganelli

2015 | Biogenesis of Enterococcis faecium biofilms

Fernanda Paganelli (1985, Sao Paulo, Brazil) received her PhD on February 26, 2015 at Utrecht University. The title of her thesis was “Biogenesis of Enterococcis faecium biofilms”. Supervisor was prof. dr. Marc Bonten and co-supervisors were dr. Helen Leavis and dr. Rob Willems (all Department of Medical Microbiology, UMC Utrecht).

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Rosa van Mansfeld

2014 | Pseudomonas aeruginosa colonization in patients with cystic fibrosis; population structure, the Dutch clone and effects of segregation

Rosa van Mansfeld (1978, Woerden) received her PhD on November 27, 2014 at Utrecht University. The title of her thesis was “Pseudomonas aeruginosa colonization in patients with cystic fibrosis; population structure, the Dutch clone and effects of segregation”. Supervisors were prof. dr. Marc Bonten (Department of Medical Microbiology, UMC Utrecht) and prof. dr. Kors van der Ent (Department of Pulmonary Diseases, Wilhelmins Children's Hospital) and co-supervisor was dr. Rob Willems (Department of Medical Microbiology, UMC Utrecht).

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Xinlin Zhang

2013 | Functional genomics of Enterococcus faecium: antibiotic resistance and niche adaptation

Xinglin Zhang (1982, Linyi, China) received his PhD on April 12, 2013 at Utrecht University. The title of his thesis was “Functional genomics of Enterococcus faecium: antibiotic resistance and niche adaptation”. Supervisor was prof. dr. Marc Bonten and co-supervisors were dr. Rob Willems, dr. ir. Willem van Schaijk (all Department of Medical Microbiology, UMC Utrecht).

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Neeltje Carpaij

2011 | A genomic approach to explore the development and evolution of methicillin-resistant staphylococci

Neeltje Carpaij (1981, Eindhoven) received her PhD on November 22, 2011 at Utrecht University. The title of his thesis was “A genomic approach to explore the development and evolution of methicillin-resistant staphylococci”. Supervisor was prof. dr. Marc Bonten and co-supervisors were dr. Rob Willems and dr. Ad Fluit (all Department of Medical Microbiology, UMC Utrecht).

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Marieke de Regt

2010 | Ampicillin-resistant Enterococcus faecium ecology, transmission and intervention strategies

Marieke de Regt (1981, Terheijden) received her PhD on December 16, 2010 at Utrecht University. The title of her thesis was “Ampicillin-resistant Enterococcus faecium ecology, transmission and intervention strategies”. Supervisor was prof. dr. Marc Bonten and co-supervisor was dr. Rob Willems (both Department of Medical Microbiology, UMC Utrecht).

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Esther Heikens

2009 | The role of Enterococcal Surface Protein in the pathogenesis of Enterococcus faecium infections

Esther Heikens (1976, Zwolle) received her PhD on December 1, 2009 at Utrecht University. The title of her thesis was “The role of Enterococcal Surface Protein in the pathogenesis of Enterococcus faecium infections”. Supervisor was prof. dr. Marc Bonten and co-supervisor was dr. Rob Willems (both Department of Medical Microbiology, UMC Utrecht).

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Antoni Hendrickx

2009 | Cell Wall-anchored Proteins of Enterococcus faecium: Exploring a Novel Surface

Antoni Hendrickx (1980, Amsterdam) received his PhD on December 1, 2009 at Utrecht University. The title of his thesis was “Cell Wall-anchored Proteins of Enterococcus faecium: Exploring a Novel Surface”. Supervisor was prof. dr. Marc Bonten and co-supervisor were dr. Rob Willems (Department of Medical Microbiology, UMC Utrecht) and dr. Willem van Wamel (Erasmus MC, Rotterdam).

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Masja Leendertse

2009 | Enterococcus faecium infections : where bacterial virulence meets innate immunity

Masja Leendertse (1976, Ouder-Amstel) received her PhD on June 18, 2009 at Utrecht University. The title of her thesis was “Enterococcus faecium infections : where bacterial virulence meets innate immunity”. Supervisors were prof. dr. Marc Bonten (Department of Medical Microbiology, UMC Utrecht) and prof. dr. Ton van der Pol (University of Amsterdam) and co-supervisor was dr. Rob Willems (Department of Medical Microbiology, UMC Utrecht).

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Helen Leavis

2007 | Evolutionary Insights into CC17 Enterococcus faecium

Helen Leavis received her PhD on December 6, 2007 at Utrecht University. The title of her thesis was “Evolutionary Insights into CC17 Enterococcus faecium”. Supervisor was prof. dr. Marc Bonten and co-supervisor was dr. Rob Willems (both Department of Medical Microbiology, UMC Utrecht).

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Janetta Top

2007 | Molecular epidemiology of Enterococcus faecium: from commensal to hospital adapted pathogen

Janetta Top (1965, Woerden) received her PhD on May 10, 2007 at Utrecht University. The title of her thesis was “Molecular epidemiology of Enterococcus faecium: from commensal to hospital adapted pathogen”. Supervisor was prof. dr. Marc Bonten and co-supervisor was dr. Rob Willems (both Department of Medical Microbiology, UMC Utrecht).

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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

T +31 (0)88-7569185

E r.willems@umcutrecht.nl