Whisk the cheese in slowly, stirring constantly to avoid clumping.
Cook bacon until crisp and remove from pan.
Add Brussels sprouts and saute on med heat until sprouts start to soften and turn brown; appx. 10 min.
Remove sprouts and set aside. In same saute pan, add ghee, garlic, and shallots, stirring to soften. Sprinkle flour over shallots and stir briskly to blend.
Add milk, whisking to combine. Slowly combine half the gruyere and parmesan to roux mixture, stirring until thick and smooth.
Place sprouts in a well greased 8"x 8" baking dish and pour cheese mixture over sprouts, topping with remaining gruyere cheese.
Bake at 400F for 20-25 min until bubbly. Top with crumbled bacon and fresh thyme before serving.