We've co-evolved for millions of years with the bacteria in our intestinal tract. These bacteria, both the continuously present intestinal microbiota and the occasional pathogenic bacteria, have great impact on intestinal health and disease.
At the division of Infectious Diseases and Immunology of the Department of Biomolecular Health Sciences, we study commensal and pathogenic intestinal bacteria, their interactions with the human or animal host, and how they contribute to health and cause intestinal inflammation and disease. Our main goal is to provide mechanistic insights into host-microbe interactions in the intestine that lead the way for the development of novel therapeutic intervention strategies.
Our main areas of focus are:
- The role of intestinal bacteria in Inflammatory Bowel Disease (Crohn's disease and ulcerative colitis)
- Enteropathogenic bacterial infections like Salmonella and Campylobacter
- The impact of the microbiota on health and disease
- Bacterial adaptation and virulence strategies in the intestinal tract
- Innate immune responses against bacterial and fungal pathogens
- The development of vaccines against intestinal bacteria
We are highly experienced with the culture of aerobic and anaerobic bacteria and multiple culturing facilities are available in the lab:
- An anaerobic chamber for culture of strict (intestinal) anaerobes.
- A culture chamber with low oxygen for microaerophilic bacteria such as Campylobacter jejuni.
- Culture jars that allow regulation of gas composition.
Bacterial infection assays
In the Infection Biology group, we have a strong track record in bacterial infection assays with different host cells. These include immune activation, adherence and invasion assays with immune cells such as macrophages or different types of epithelial cells. Assay read outs include bacterial enumeration, FACS, ELISA, NF-kB activation, qRT-PCR or microscopy (confocal, live or SEM).
CRISPR/Cas9 genome editing
CRISPR/Cas technology is revolutionizing the field of molecular biology. We are applying this technique to target genes of interest in mammalian cells to create knockout cell lines. Introduction of targeted mutations or epitope tags is also feasible using our strategy.
Next-generation sequencing of DNA samples of single bacteria or complex microbiota is performed by the Utrecht Sequencing Facility (http://useq.nl).
IgA-SEQ is a technique to identify intestinal pathobionts that are associated with inflammation. IgA-SEQ is performed by Dr. Marcel de Zoete (UMC Utrecht).
Sortagging is a method of protein ligation that allows site-specific attachment of different probes, e.g. fluorescent molecules or biotin handles. The technique is making use of the sortase enzyme of Streptococcus pyogenes that cleaves at a short recognition sequence (LPETG) and can attach a glycine-based nucleophile (GGG-Biotion, GGG-Alexa647). Sortagging can also be performed on the surface of live cells. Labeling of surface receptors with biotin can facilitate immunoprecipitations and reduce background noise to allow identification of interaction partners.
C.C.I - Center for Cell Imaging
The Center for Cell Imaging (CCI) is a multi-user facility offering advanced microscopic techniques to scientists of the Faculty of Veterinary Medicine and other faculties affiliated with the Utrecht Life Sciences.
Microscopes available at CCI:
– Leica TCS SPE-II confocal laser scanning-microscope on a DMI4000
– Olympus BX60 fluorescence mic with color CCD camera (Leica DFC425C)
– GE Healthcare OMX-V4 blaze Live cell super resolution using SIM
– NIKON STORM/A1Rsi/TIRF Live cell system with superresolution possibilities
– Zeiss SLM880 NLO Multiphoton microscope for in vivo imaging