A composition and method for immunizing a mammal infected with Mycobacterium are disclosed. The genes gcpE, pstA, kdpC, papA2, impA, umaA1, fabG2_2, aceAB, mbtH2, IpqP, map0834c, cspB, lipN, and map1634 of M. paratuberculosis and the products that they encode are vaccine targets for Johne's and Crohn's disease. Eighteen M. paratuberculosis-specific genomic islands (MAPs) were identified. Three inverted large genomic fragments in M. paratuberculosis (INV) were also identified. These genomic identifiers represent novel virulence determinants that can be used as targets for vaccines and for developments of drugs against Johne's disease. The methods can be used to deliver an immunizing compound to a mammal, to provide an immune response against Johne's or Crohn's disease in the mammal.