Germ-Free and Gnotobiotic Mouse Facility Ghent (GFMF)

Vereecke Lars

Vereecke Lars

Research Teamleader
Head of Core Facility
Andries Vanessa

Andries Vanessa

GFMF Coordinator

Germ-Free and Gnotobiotic Mouse Facility Ghent (GFMF)


The GFMF is an excellence center for functional microbiota research. The facility contains one large germ-free mouse breeding unit (>10 isolators), where germ-free C57Bl6/J, Swiss-Webster and multiple transgenic mouse lines are bred. In addition, the facility contains a gnotobiotic unit equipped with positive-pressure isocages and experimental isolators in a BSL3 environment.

The GFMF provides service for scientists at VIB-IRC and Ghent University, and for the broader scientific community in Flanders and beyond. The germ-free facility provides support to design your germ-free and gnotobiotic experiments, and trains scientists to work in the facility. Various animal experimental procedures can be organized, including colonization experiments (mono-associations, minimal consortia and complex microbiota transplantations), diet interventions, infection experiments, disease modelling (IBD, arthritis, diabetes, colorectal cancer…etc).

The GFMF provides following services:

• Supply germ-free C57Bl6/J mice for experimental procedures in the GFMF, IRC or external institutes (including germ-free shipping procedures)

• Support for custom made germ-free and gnotobiotic experiments (after ethical approval by the UZ Ghent ethics committee)

• Germ-free rederivation of transgenic mouse lines, in collaboration with IRC Trasgenic Core Facility, and subsequent germ-free breeding in the GFMF or shipment to external institutes

• Training of scientists for germ-fee and gnotobiotic experiments

• Cultivation of bacteria for gnotobiotic experiments in either aerobic or anaerobic conditions

• Sterility testing

• DNA extractions for metagenomics analyses in clean room environment

• Technical consultation

• Other services may be available on request

The state of the art GFMF infrastructure includes:

Custom built laminar flow cabinet for germ-free surgery, Experimental set up for germ-free embryo transfer, Gnotobiotic facility for colonization experiments (mono-association, microbial cocktails, FMT,…), Mouse anaesthesia device (isoflurane) for germ-free and gnotobiotic experiments, Mouse colonoscopy set up for germ-free and gnotobiotic experiments, Aerobic and anaerobic cabinets for bacteriology and tissue processing.

Selected publications

  • Thiran, A. et al. Sterile triggers drive joint inflammation in TNF and IL-1b dependent mouse arthritis models. EMBO Molecular Medicine, in press (2023).
  • Xie, J. et al. Gut microbiota regulates blood-cerebrospinal fluid barrier function and Abeta pathology. EMBO J, e111515 (2023). Visit ➚
  • Degraeve, A. L. et al. Gut microbiome modulates tacrolimus pharmacokinetics through the transcriptional regulation of ABCB1. Microbiome 11, 138 (2023). Visit ➚
  • Wynendaele, E. et al. The quorum sensing peptide EntF* promotes colorectal cancer metastasis in mice: a new factor in the host-microbiome interaction. BMC Biol 20, 151 (2022). Visit ➚
  • Villar, V. H. et al. Hepatic glutamine synthetase controls N(5)-methylglutamine in homeostasis and cancer. Nat Chem Biol 19, 292–300 (2023). Visit ➚
  • Anderson, C. J. et al. Microbes exploit death-induced nutrient release by gut epithelial cells. Nature 596, 262-267 (2021). Visit ➚
  • Slowicka, K. et al. Zeb2 drives invasive and microbiota-dependent colon carcinoma. Nature Cancer 1, 620-634 (2020). Visit ➚
  • Van Hove, H. et al. A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment. Nat Neurosci 22, 1021–1035 (2019). Visit ➚

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