Microbiomics - Group Paganelli
Microbiomics - Group Paganelli


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.

Research program

Infection and Immunity

Research interests

Host-bacteria interactions


Fernanda Paganelli

Phone: +31 0887553979

Related websites

Group members

Research technician


Malbert Rogers

PhD student

Paul Stege

Join our group

Bachelor and master students

Opportunities to work with microbiome profiling and host bacteria interactions using organoid models.

Key publications

  1. Low-calcium diet in mice leads to reduced gut colonization by Enterococcus faecium. Top J, Hendrickx APA, van Ampting MTJ, van Limpt K, Knol J, van de Kamer D, Braat JC, Viveen M, Rogers MR, Kemperman H, Willems RJL, Paganelli FL.Microbiologyopen. 2019 Sep 30:e936. doi:10.1002/mbo3.936. View
  2. In vivo acquisition of fosfomycin resistance in Escherichia coli by fosA transmission from commensal flora. Ten Doesschate T, Abbott IJ, Willems RJL, Top J, Rogers MRC, Bonten MM, Paganelli FL. J Antimicrob Chemother. 2019 Sep 11. pii: dkz380. doi:10.1093/jac/dkz380. View
  3. Roux-Y Gastric Bypass and Sleeve Gastrectomy directly change gut microbiota composition independent of surgery type. Paganelli FL, Luyer M, Hazelbag CM, Uh HW, Rogers MRC, Adriaans D, Berbers RM, Hendrickx APA, Viveen MC, Groot JA, Bonten MJM, Fluit AC, Willems RJL, Leavis HL. Sci Rep. 2019 Jul 29;9(1):10979. doi: 10.1038/s41598-019-47332-z. View
  4. Is Microbiota Research Advancing Our Understanding of Infection? Paganelli FL, Ekkelenkamp MB. Clin Infect Dis. 2019 Apr 8;68(8):1300-1302. doi: 10.1093/cid/ciy712. View
  5. Group IIA-Secreted Phospholipase A2 in Human Serum Kills Commensal but Not Clinical Enterococcus faecium Isolates. Paganelli FL, Leavis HL, He S, van Sorge NM, Payré C, Lambeau G, Willems RJL, Rooijakkers SHM. Infect Immun. 2018 Jul 23;86(8). pii: e00180-18. doi:10.1128/IAI.00180-18. View


UMC Utrecht

Jeffrey Beekman, Prof, WKZ
Onno Kranenburg, Prof
Jurgen Kuball, MD/PhD
Linde Meyaard, Prof
Femke van Wijk, PhD
Marjolein de Bruin-Weller, MD/PhD
Gaby Steba, PhD
Karijn Suijkerbuijk, MD/PhD
Hae-Won Uh, Julius Center

Utrecht University

Aldert Zomer, PhD, Veterinary faculty
Dr. Aldert Zomer
Dr. Bas Dutilh

Prinses Máxima Center for Pediatric Oncology

Caroline Lindemans, MD/PhD

Exeter University

Stineke van Houte, PhD




2018 - University Medical Center Utrecht

Speerpunt Infection & Immunity grant


UMC News

8 Aug 2019 - Maagverkleining bij ernstig overgewicht verandert samenstelling van de darmflora

Education & Courses

BSc Biomedical Sciences

Molecular Biology of Bacterial Infections

MSc Infection and Immunity

Bacterial Pathogenesis

Summer Course: I &I summer school Utrecht University