The present invention relates to Mycobacterium avium subspecies paratuberculosis (MAP) as the etiological agent of IBD, including ulcerative colitis and Crohn's disease, as well as Multiple Sclerosis and Alzheimer's Disease. As such, methods for monitoring efficacy of a anti-MAP therapy and determining whether a blood sample is suitable for transfusion are provided based upon presence, absence or amount of MAP nucleic acid.