T4 Bacteriophage and E. coli Interaction in the MurineIntestine: A Prototypical Model for Studying Host-Bacteriophage Dynamics In Vivo

Bacteriophages (phages) are viruses that infect bacteria with species- and strain-levelspecificity and are the most abundant biological entities across all known ecosystems.Within bacterial communities, such as those found in the gut microbiota, phagesare implicated in regulating microbiota population dynamics and driving bacterialevolution. There has been renewed interest in phage research in the last decade, inpart due to the host-specific killing capabilities of lytic phages, which offer a promisingtool to counter the increasing threat of antimicrobial resistant bacteria. Furthermore,recent studies demonstrating that phages adhere to intestinal mucus suggest they mayhave a protective role in preventing bacterial invasion into the underlying epithelium.Importantly, like bacterial microbiomes, disrupted phageomes have been associatedwith worsened outcomes in diseases such as inflammatory bowel disease. Previousstudies have demonstrated that phages can modulate the microbiome of animalsand humans through fecal filtrate transplants, benefiting the host's health. With thisrecent wave of research comes the necessity to establish and standardize protocolsfor studying phages in the context of the gut microbiome. This protocol provides a set ofprocedures to study isolated T4 phages and their bacterial host, Escherichia coli, in thecontext of the murine gastrointestinal tract. The methods described here outline howto start from a phage lysate, administer it to mice and assess effects on bacterial hostand phage levels. This protocol can be modified and applied to other phage-bacterialpairs and provides a starting point for studying host-phage dynamics in vivo