1. Preheat oven to 350 degrees F. Spray cookie sheet with nonstick cooking spray, lay eggplant out on the sheet, and bake until soft (15-20 minutes).
2. While eggplant is baking, saute onions and garlic in a nonstick skillet with a tablespoon of water until soft (5-6 minutes).
3. Stir together the cheeses in a small bowl. In a separate bowl, stir together the wheat germ and spices.
4. Coat a 13"x9" baking dish with nonstick cooking spray and create layers of eggplant, onion, cheese, tomato, and wheat germ, making the final layer wheat germ. Bake until heated through and browned on top (25-30 minutes).