Single-Cell Genomics Resolution of Microbe-Virus Interactions in IBD.

The microbes that colonize the human intestine, collectively known as the gut microbiome, are critical players in many human diseases including IBD. Patients with IBD often have fewer different types of intestinal bacteria and an increase in certain types of bacteria associated with inflammation. In addition to bacteria, there are many viruses that live in the human gut. Small viruses called bacteriophages can infect the gut bacteria, causing substantial changes to bacterial populations. IBD patients have expanded populations of bacteriophages, which may play a role in disease. While bacteriophages are important in IBD, a critical hurdle is that our knowledge of the diversity of different phages, and which bacteria they infect, is extremely limited. We will use a new technique that allows us to look at single intestinal bacteria and carefully analyze the virus(es) that infect them. This will allow us to better understand the predator-prey relationships they share with bacteria. These studies will provide important insight into the complex interactions between bacteria and bacteriophages in the microbiome, and help us understand how and why these interactions are altered in IBD. Ultimately, these findings will facilitate development of probiotic and phage therapies for IBD.