There is speculation that the bacterium, Mycobacterium avium paratuberculosis (MAP), is a causative agent of Crohn's disease (CD). Current diagnostic techniques for MAP are poor. Therefore, it is crucial that we devise new assays to detect for MAP in CD patients. To gain insight into the relationship between MAP and CD, we must sequence the MAP genome and isolate it from CD patient blood. Genomic isolation techniques include PCR amplification and the novel use of hybrid capture probes.