In a small trial of fecal transplants in patients with inflammatory bowel disease, my colleagues and I sought to answer two questions: (1) What bacteria, viruses, genes, and molecules colonize recipient patients? (2) How does the new host respond? I led analysis and generation of data from stool, blood, and biopsies: 16S, metagenomics, bacterial isolates, whole-genome sequencing, viral sequencing, single-cell RNA sequencing, immune repertoire sequencing, immunoglobulin-A sequencing, and metabolomics.
Before we can understand how to harness the immune system to diagnose and treat disease, we must first understand its internal dynamics. Using ecological principles, I studied the longitudinal dynamics of the immune system (specifically the T-cell and B-cell receptor repertoire) in patients and healthy controls.
My colleagues and I are developing a next generation of diagnostics, which moves beyond the disease-biomarker paradigm to instead focus on actionable, data-driven clinical decisions using high-throughput data such as metabolomics.
My colleagues and I identified a prophage-driven mechanism for hypermutation present in a diverse array of clinical and environmental bacteria.
As a U.S. Fulbright Fellow, I used metagenomics to study the distribution of bacteria and pathogens across reef-building corals in the Caribbean.
I identified a genetic population structure in a marine snail that mirrored the snail’s colonization history and possible thermal adaptation.