This proposed research program will determine the microbial constituents of tissues associated with inflammatory bowel diseases (IBD), in both human and animal systems, in order to identify microbes associated with the disease-states. The human inflammatory bowel diseases, ulcerative colitis (UC) and Crohn?s disease (CD), are chronic, devastating diseases of unknown etiology. It is possible that microorganisms, perhaps indigenous and so far undiscovered, participate in the disease process. Although some evidence suggests that Mycobacterium avium ssp. paratuberculosis (MAP) may be involved in CD, microbiological analyses have been critically compromised by the clinical need to culture unknown organisms in order to detect and identify them. Culture techniques are frequently ineffective and usually underestimate the true diversity of microbes in natural samples. The phylogenetic analysis of ribosomal RNA (rRNA) genes, amplified from mixed community genomic DNA (e.g. host plus associated microbiota) by polymerase chain reaction, allows species identification in the absence of cultivation. We propose to analyze the microbial communities of both human IBD and normal gastrointestinal samples by this rRNA gene-based technology in order to identify and characterize candidate microbial etiological agents of IBD. The results of molecular studies will guide directed attempts to culture suspected pathogens, including MAP, from diseased tissues. Parallel analyses of animal IBD models, including bovine Johne?s disease and rodent models of IBD, will be conducted in order to validate the molecular-phylogenetic strategy, provide insight into microbial involvement in IBD pathogenesis, and guide the choice of appropriate tissues to be analyzed in human IBD.