Understanding the role of phages in the mammalian gut microbiome

Abstract

A healthy gut microbiome supports a stable microbial community that regulates immune responses, defends against pathogens, maintains gut barrier integrity, and modulates metabolic processes. Disruptions of the balanced microbial community, followed by effects on host health, often called dysbiosis, have been associated with alterations in phage composition. However, whether these changes are correlational or causative has remained unresolved for many years. The complex tripartite interactions within the gut microbiome between phage, bacteria, and host health are difficult to study. To study these interactions within the gut microbiome, murine models have been beneficial through manipulation of the gut. Gnotobiotic mice have been used to look closely at the interactions between bacteria and phage and the effect on host metabolism. However, these models are limited, using only a defined set of host-phage pairs, as recapitulating the dynamic and diverse nature of the gut microbiome comes with difficulty. In this context, multiple studies were conducted to elucidate the role of phages within the gut microbiome and their impact on host health. The significance of phage in the gut microbiota remains poorly understood due, in part, to the absence of an animal model that allows for a comparative study of conditions with or without phages while retaining the microbial diversity attained by conventional colonization. In Chapter II, we describe the development of a murine model, the bacteriophage-conditional mouse model (BaCon), that manipulates endogenous gut phage, shedding light on how the viral community impacts the microbial community and host health. Initially, we describe a mouse model that uses a broadly available chemical compound, acriflavine, to preferentially deplete virulent phages from the gut. We then show that gut phage density can be reconstituted by oral gavage. Using the BaCon mouse model, we revealed that while phages have comparatively minimal impact during equilibrium conditions, they can increase the potency of ampicillin against commensal gut bacteria. Collectively, our work identifies virulent gut phages as potential sources of bacterial variability during significant perturbations. The murine model analysis was done using in vitro and in vivo experiments, laboratory culturing experiments, and metagenomic analysis, including 16S rRNA and whole virome sequencing. Through the manipulation of gut phage by acriflavine, we wondered if there could be more compounds that impact phage. In Chapter III, we screened two compound libraries from Targetmol (2,484 compounds) and APExBIO (2,726 compounds) against E. coli and T4 phage. We identified compounds from different drug classes, particularly at low concentrations (15 µM and 50 µM), that inhibited or enhanced phage activity. In future studies, we plan to test these identified compounds against additional host-phage pairs in vitro and evaluate these compounds in an in vivo mouse model, assessing potential disruption to the gut phage community and microbiota. This research suggests that phage impacts the microbial community and host health.