Intestinal phage metagenomics
In collaboration with Dr. Manuel Kleiner's lab, we are employing metagenomics and mouse models to decipher how bacteriophages (phages) are impacted by host inflammation and whether phages promote dysbiotic bacterial communities in the intestine. Using a sequence database independent approach for the selection of phage genomes, we discovered that intestinal phage communities transition from an ordered state to a stochastic dysbiosis during colitis (Duerkop, Kleiner et al. 2018). We identified phages specific to pathobiotic hosts associated with intestinal disease to be elevated during colitis. Additionally, phages in healthy and diseased mice overlapped with phages from healthy humans and humans with Inflammatory Bowel Disease. We continue to explore how host environmental ques shape intestinal phage communities and how phages influence intestinal inflammatory diseases.