Preheat the oven to 400 degrees F and grease three ramekins with butter and coat with the freshly grated parmesan on the bottoms and sides.
In a small saucepan, heat the milk with the two sprigs of thyme on low heat until steaming.
In a separate small saucepan, melt the butter over medium heat. Once melted, add in the flour and constantly stir for about 2-3 minutes or until it begins to foam.
Remove the butter, flour mixture from heat and pour in the warm milk (remove the sprigs of thyme). Stir mixture to combine, then return to medium heat and stir constantly for another 2-3 minutes until thick.
Remove from heat and stir in the salt and pepper.
Transfer to a medium bowl to cool for about 1-2 minutes.
Next, add in the egg yolks one at a time, stirring to fully combine before adding the next one. Allow to cool completely.
Meanwhile, place the egg whites in a medium bowl and beat with an electric mixer until stiff peaks form.
Fold 1⁄4 of the egg whites into the souffle mixture until no lumps of whites remain.
Fold another 1⁄2 of the whites into the mixture, as you sprinkle in half of the gruyere cheese and half of the sauerkraut.
Repeat with the remaining egg whites, cheese, and sauerkraut.
Divide the mixture up between the three ramekins.
Place the souffles in the oven and immediately reduce the temperature to 375 degrees F.
Bake for about 20-22 minutes or until they are puffed up, the tops are golden brown, and the centers only slightly giggle when shaken. (Do NOT open the oven door for the first 20 minutes)
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