I feel that the study of prehistoric pathogen genomes may provide some insight into the development and progression of pathogenesis over time. Although not considered prehistoric, the genomic research and subsequent reverse genetic analysis conducted on samples of the 1918 flu taken from the lungs of individuals that died led to several conclusions regarding the role of specific non-structural proteins that serve as pathogenicity factors. It will be essential, however, that studies conducted look not just at single prehistoric samples, but paint a continuous history to the modern age. By having a historical reference for genetic modifications, the relevance and persistence of such changes may identify selected conserved epitopes associated with infectivity and pathogenicity. 

In regards to the use of past microbiomes as novel vaccine targets, I feel that this approach may be far more difficult. The microflora including the prominent pathogenic species afflicting human and other animal species have likely changed dramatically since prehistoric times. From a standpoint of vaccine design, the key question is whether the antigenicity of prehistoric populations would overlap at all with modern pathogens and be able to confer any protective immunity. Depending upon the pathogen, it may, however for many microbes including most viruses which undergo rapid evolution there is good chance that it will not.