Bacterioph00ages for gut health

Bacteriophages (phages), viruses that specifically target and infect bacteria, are a major component of the gut microbiome, but they are not as well-studied as their bacterial hosts. Recent high-throughput sequencing approaches have revealed tens of thousands of different phage species in the healthy gut. These phages continuously interact with each other and their bacterial hosts, but we have very limited information on how they interact with the cells of the human gut. Previous studies on individual bacteriophages raised the possibility that the gut epithelium can act as a sink for bacteriophages, while other studies showed a range of gut epithelial responses differing from phage to phage. What we currently have no information on, is how phage communities as a whole interact with the human gut epithelial environment. In this project, we will take advantage of the availability of gut microbiome studies and human biopsy-derived intestinal organoid-based cell models at our Institute to investigate phage-gut interactions with the epithelium.

The gut microbiome studies currently running at the Quadram Institute Bioscience (QIB), the PEARL study (investigating the role of the gut microbiome in pregnancy and early life) and the MOTION study (investigating the role of the gut microbiome in older adults), will allow us to use microbiome sequencing information and the associated faecal samples to generate natural human gut phage communities. These communities will then be tested on biopsy-derived culture models of human gut cells, called organoids, that mimic the gut environment. More specifically, we will combine the phage communities with the human gut organoids and monitor the changes over time for both the phage communities and the human gut cells. Using high-throughput sequencing and qPCR, we will quantify the changes in phage community composition and structural protein content, and track phages across the cell monolayer. We will investigate the cellular response by looking at markers of gut barrier function. In parallel, we will develop a phage biobank of cultured isolates that can be used in the future for the biocontrol of gut-associated bacterial pathogens or for the modulation of the gut microbiome. Informed by the data on the phage-gut interactions, we will assemble cocktails of different phages that are most suited for use in the human gut, and test these on our gut organoid system.

This study will increase our functional understanding of bacteriophages as part of a healthy gut microbiome. Through the identification of the phage types that are most adapted to the gut environment and the response of the gut epithelium, we will be able to form a more comprehensive picture of phage-gut interactions. In addition, the findings will allow us to make better informed decisions on the appropriateness of specific phage types for potential application as therapeutics.

Bacteriophages (phages) are an integral part of the healthy gut microbiome, but little is known of how natural gut phage communities interact with human gut epithelial cells. In this study, we will use 2D organoid models derived from human intestinal biopsies to investigate the interactions between phages and the gut epithelium. We will investigate infant and adult faecal-derived phage communities from two cohort studies at the Quadram Institute Bioscience, providing unique and well-characterised sets of natural gut phages. Organoids will be grown on Transwells and seeded with faecal-derived phage communities specifically designed and characterised for this project. Using shotgun metagenomics of the viral communities and qPCR, we will determine the distribution of phages within the intestinal epithelium and identify the structural protein features associated with differential responses. In parallel, we will investigate what the cellular response is to these natural communities, using shotgun transcriptomics of the cellular fraction of the organoid models and multiplex ELISA of inflammatory markers, followed by validation with qPCR and Western blot of specific markers. We will specifically be investigating gut barrier function and phage community composition. The findings of the interactions will be used to inform the selection and development of phage cocktails most relevant for use in the human gut, and these will be tested and validated on the organoid-derived model. This project will advance our fundamental understanding of the interactions between phages and the human gut that will be exploited to improve the selection of phages for therapy.