PROJECT SUMMARY Inflammatory Bowel Diseases (IBD), consisting of Ulcerative colitis (UC) and Crohn's disease (CD), are chronic progressive inflammatory conditions of the intestine. Numerous lines of evidence suggest their origins lie in an overaggressive response of the host immune system towards the gut microbiota in a genetically susceptible host. We hypothesize a key feature of IBD is the persistent colonization by colitogenic microbial strains in the absence of sufficient colitoprotective strains that over years to decades can drive the progressive inflammation and damage associated with IBD. To test this hypothesis we propose three Aims. In Aim 1, we will sample, every year for five years, the fecal microbiota of individuals with Inflammatory Bowel Disease (UC or CD) and healthy controls. To understand the implications of gut microbiota stability in the context of a gut microbiota manipulation intervention, we will also longitudinally sample recipients of fecal microbiota transplantation (FMT) for ulcerative colitis, after FMT therapy has ended, for up to 5 years. We will use metagenomics combined with high throughput microbial isolation and genome sequencing to identify the stable and transient microbes in each individual's microbiota and determine if individuals with IBD have significantly altered gut microbiota stability. We will also track the loss of engrafted FMT donor strains in subjects in remission post-FMT overtime to associate strain loss with long-term-relapse. In Aim 2, we will use gnotobiotic T-cell transfer colitis mice colonized with subsets of each microbiota to identify colitogenic and colitoprotective microbial strains and to determine if colitogenic or colitoprotective organisms are preferentially found in the stably colonized community members. We will also determine if colitogenic and colitoprotective strains drive unique baseline immune tones when colonized in unchallenged gnotobiotic mice. With an aim towards future human translation, we will search for minimal colitoprotective subsets from previously identified colitoprotective communities, and we will determine if strains lost post-FMT are colitoprotective, in UC subjects that achieve remission but subsequently relapse. Together these aims will help us determine if individuals with Inflammatory Bowel Disease are enriched in stably colonized colitogenic organisms whose elimination might form a novel therapeutic intervention for the treatment or prevention of Inflammatory Bowel Disease and if healthy individuals are enriched in stably colonized colitoprotective organisms that might form the basis of a novel IBD therapeutic.