We are employing metagenomics and mouse models to decipher how bacteriophages (phages) are impacted by  inflammatory diseases 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, we discovered that unique intestinal phage signatures are associated with humans at risk for developing rheumatoid arthritis (Mangalea et al. 2021)  We continue to explore how host environmental ques shape intestinal phage communities using novel bioinformatic techniques (Kleiner et al. 2020) and how phages influence intestinal inflammatory diseases. Together these studies will lead to novel approaches for the manipulation of microbiotas relevant to human health (Kirsch et al. 2021).