Human Gut Microbiome in Crohn's Disease

Inflammatory bowel diseases (IBD), such as Crohn's disease, are chronic, immunologically mediated disorders that have severe medical consequences. The current hypothesis is that these diseases are due to an overly aggressive immune response to a subset of commensal enteric bacteria. Studies to date on IBD have suggested that the disorder may be caused by a combination of bacteria and host susceptibility; however the etiologies of these diseases remain an enigma. In this application, we propose to develop and demonstrate the ability to profile Crohn's disease at an unprecedented molecular level by elucidation of specific biomarkers (bacterial strains, genes, or proteins) that correlate to disease symptoms. To achieve this goal, we will employ a multidisciplinary approach based on metagenomic and metaproteomic molecular tools to elucidate the composition of the commensal microbiota in monozygotic twins that are either healthy or exhibit Crohn's disease (for concordant, both are diseased; for discordant, one is healthy and one is diseased). The central hypotheses of this proposal are (1) that specific members and/or functional activities of the gastrointestinal (GI) microbiota differ in patients with Crohn's disease as compared to healthy individuals, and (2) that it will be possible to elucidate microbial signatures which correlate with the occurrence and progression of this disease by integration of data obtained from 16S rRNA-based molecular fingerprinting, metagenomics, and metaproteomics approaches. To address these hypotheses, three specific aims are proposed: 1) Obtain data on community gene content (metagenome) in a subset of healthy twins and twins with Crohn's Disease to assess potential differences in the metabolic capabilities of the gut microbiota associated with CD, 2) Obtain data on community protein content (metaproteome) in a subset of healthy twins and twins with Crohn's Disease to assess the state of expressed proteins associated with CD, 3) Apply various statistical clustering and classification methods to correlate/associate microbial community composition, gene and protein content with patient metadata, including metabolite profiles and clinical phenotype. The ultimate goal of these efforts is to identify novel biomarkers for non-invasive diagnostics of CD and to eventually identify drug targets (i.e. bacterial strains) for cure or suppression of disease symptoms. PUBLIC HEALTH RELEVANCE: This study aims to unravel the contribution of the bacteria that normally inhabit the human gastrointestinal tract to Crohn's disease by using a multidisciplinary approach to study changes in the structure and function of gut microbial communities in three sets of patient cohorts who have Crohn's disease. These results will be compared with those obtained from the study of healthy individuals and have the potential to identify new biomarkers of disease severity, location, and progression.]]> Questionnaire: Exclusion criteria for participating in dietary intervention studyRESEARCH RECONSENT FORMQuestionnaire: Information to accompany stool sample for dietary intervention studyProtocolMetagenomic sequence data will be obtained from fecal DNA collected from five twin pairs: two concordant, two discordant and one healthy twin pair that have been extensively characterized with regard to in-depth microbial community fingerprints and clinical data related to the onset of CD. All of the patient recruitment efforts strived to include an equal representation of men and women. We do not plan to study children as the procedures involved in the clinical study are inappropriate for children.]]> Inflammatory bowel diseases (IBD) are increasing in prevalence in Europe and North America (current estimates are approximately 0.4% of the population (Loftus, 2004, PMID: 15168363), which likely is due in part to the Western lifestyle. IBD can be divided into two categories: Ulcerative Colitis (UC) and Crohn's Disease (CD). Both are chronic, relapsing, immunologically mediated disorders that can have severe physical consequences. This study describes research that will combine state-of-the-art experimental and computational methods to characterize variation in the gut microbiota in CD at a level never before possible. At the present, there are virtually no other reports that have addressed the complex aspects of this severe disease by studying both microbial community structure and function. A microbial involvement in the etiology of CD has been suggested, characterized, in part, by an imbalance between beneficial and detrimental bacteria in the intestine microbiota between healthy individuals and CD patients. Given that we do not currently understand whether changes in the types and/ or abundance of microbial community members, or changes in gene content, or changes in level of expressed protein (or some combination of the three) are most relevant to the etiology of CD, we believe it is essential to take a more holistic view of this question and examine microbial community structure and function. Version 2 of this study was created so that new subjects and sample data could be added. Version 3 of this study serves to incorporate 16S sequencing data for new subjects and samples as well as add 16S data to several previously registered subjects for whom WGS data have also been submitted.]]>