Welcome to our website! The van Houte lab is based in the Environment and Sustainability Institute at the University of Exeter’s Cornwall Campus.  The Van Houte lab studies interactions between genetic parasites (mainly bacteriophages and plasmids) and their bacterial hosts, with a particular focus using CRISPR-Cas, an adaptive immune system in bacteria, to remove antimicrobial resistance genes from microbial communities.

Below you will find an overview of the current themes we work on:

CRISPR-Cas as antimicrobials. Antimicrobial resistance (AMR) poses a tremendous challenge to our society. Several pioneering studies have shown that CRISPR-Cas can be used to eradicate genes encoding AMR from microbial communities. However, this technology has only been tested under laboratory conditions, and there are still many hurdles to take before it can be used in the real world (see our Pearl in Plos Pathogens). Together with Will Gaze from the University of Exeter Medical School and Marie-Curie fellow Uli Klümper, our current research focuses on developing new ways to use CRISPR-Cas to eradicate AMR genes from a complex microbial community. We focus on various different model systems:

  1. Pig gut-derived microbial communities (BioMed DTP funded PhD student David Walker-Sünderhauf)
  2. Vancomycin-resistant Enterococcus faecium and multidrug-resistant Enterobacteriaceae (ERC/CLES-funded PhD student Ellie Pursey, this project is in collaboration with Dr Fernanda Paganelli at UMC Utrecht, the Netherlands)
  3. A stable five-species microbial community established by the Buckling lab (BioMed DTP funded PhD student David Walker-Sünderhauf)

Large-scale genomic associations between MGEs and bacterial immune system (PhD student Ellie Pursey) Check out our latest preprint on this work here!

Co-evolutionary dynamics between bacteriophages and their bacterial hosts. We work with several different model systems, including Pseudomonas fluorescens and its phage phi2 (in collaboration with Angus Buckling), Pseudomonas aeruginosa strain UCBPP-PA14 and its phage DMS3 (in collaboration with the Westra lab), and Streptococcus thermophilus and its phage 2972.

Interactions between CRISPR-Cas immune systems and phages encoding anti-CRISPRs. Several years ago it was discovered that some phages encode small proteins that are able to block CRISPR-Cas immunity. Over the past few years we have studied the epidemiology of these anti-CRISPR-phages. Funded by a BBSRC New Investigator Award and in collaboration with the Pagliara lab we study how anti-CRISPR phages work together to overcome CRISPR-Cas immunity (with postdoc Benoit Pons and technician Matthew Chisnall).

We share lab facilities and collaborate with the Westra lab, the Buckling lab and the European Centre for Environment and Human Health