Objective: The challenge in the post-genome era to interpret bioinformatics research is significant and useful to confirm therapeutic targets and to develop medical applications. To develop evidence-based medicine, virulent factors of periodontal pathogen were identified by genome science technology, and safer and useful passive antibodies inhibiting molecular target functions were constructed. Methods: Gene and protein expressions of virulent factors in P. gingivalis were analyzed by a custom-made DNA microarray and 2D SDS-PAGE/MALDI-TOF MS. Recombinant proteins or functional domain peptides of molecular targets were immunized to mice and constructed mAbs inhibiting virulent activities. Single-chain variable fragment (ScFv) genes from the hybridoma were molecular cloned and expressed in bacterial hosts. Human type mAbs were constructed by hybridoma technology using transgenic mice carrying human IgG gene loci. IgY was prepared from the egg yolk of immunized hens. Results: Homology search of genome database, microarray and proteomic analysis demonstrated new function and usefulness of molecular targets. The constructed safer passive antibodies against molecular targets were capable neutralizing virulent activities. Conclusions: Genome scienceÐbased gene expression monitoring and proteomic analysis are useful to identify potential gene and protein for immunotherapy, and ScFv, human mAbs, IgY, which are capable inhibiting virulent factors will be useful to prevent oral infectious diseases.