Our laboratory studies the gut microbiome, with specific foci on host diet, bacterial pathogens, and bacteriophages. Our overall goal is to build novel concepts and approaches for mitigating pathogen-infested or otherwise problematic microbiomes. This work is especially important given the burgeoning antibiotic resistance crisis and our growing awareness of the myriad ways microbes impact our health. Our work leverages a broad toolkit including bacterial genetics, multiple “omics” analysis, and murine models of human disease.

Two questions that we’re especially excited about now:

How does diet impact pathogen fitness? Host diet is one of the most tractable ways to affect the composition and functionality of the gut microbiome. We seek to understand how diet-driven changes to the microbiome impact infection by pathogens, including Clostridioides difficile. This work will yield a framework for the development of orthogonal approaches (distinct from antibiotics or fecal transplant) for mitigating C. difficile and other gastrointestinal pathogens.

How can bacteriophages be leveraged therapeutically? As we face the growing threat of antibiotic resistance, the revival of bacteriophage (phage) therapy is an attractive option to help in our recovery from this crisis. Importantly, unlike antibiotics, phages target bacteria with strain-level specificity and can be used without inflicting collateral damage on the microbiome. However, despite past triumphs and promise for the future, phage therapy is inconsistently effective, in large part due to an incomplete understanding of how phages behave in complex, host associated microbial communities. To build this necessary understanding, we leverage controlled experimental systems to understand the diversity, ecological impacts, and therapeutic potential of phages.