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Heat milk, thyme, shallot and bay leaf till it bubbles and simmers, then remove from heat and allow to steep for one hour. Strain milk through a fine strainer and set aside.
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Preheat oven to 375°F.
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Melt butter in a heavy bottom sauce pan over medium heat. Add flour and whisk to combine. Reduce heat to low and cook for 3 minutes, stirring continuously. Add the steeped milk all at once. Stir continuously till mixture is bubbly and thickened.
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Remove from heat and add egg yolks, stir well till completely incorporated. Add Parmesan and goat cheese and stir to combine. It's okay if some small pockets of goat cheese remain.
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Place egg whites in a clean, medium size bowl and beat with an electric mixer till stiff peaks form. Add ¼ of the egg whites to the cheese mixture and fold gently from the bottom up. Add half of the remaining egg whites and fold until combined. Repeat with remaining whites. Mix gently till combined.
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Scoop batter into prepared, pre-baked shells. Top with sliced tomatoes. Brush surfaces of tomatoes gently with olive oil. Sprinkle with freshly ground black pepper.
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Place sheet pan in oven and bake until soufflés are puffed and light golden brown, about 20 minutes. Serve immediately or keep at room temperature for 3-4 hours. Reheat for 8-10 minutes at 375˚F before serving.
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Garnish with fresh thyme leaves, if desired