1. Preheat the oven to 400 degrees F.
2. In a medium saucepan, warm the olive oil over medium-high heat. Add the shallot and saute until soft. Add the mushrooms and cook until softened. Fold in the thyme.
3. Grease four (8 oz.) ramekins with cooking spray and place on a baking sheet.
4. Beat the eggs with the milk, salt and pepper. Divide the mushroom mixture evenly between the ramekins. Layer cheese on mushrooms and top with egg mixture.
5. Place baking sheet in the oven and cook for 20 to 25 minutes, or until the tops are golden