In a large non-stick skillet, cook the bacon over medium heat until crispy, about 6-8 minutes. Transfer to a paper towel-lined plate to drain excess fat, reserving 1 tablespoon of the bacon grease in the skillet.

Add the diced yellow onion to the skillet and sauté over medium heat for about 3 minutes until softened. Stir in the grated garlic and baby spinach, cooking for an additional 2-3 minutes until the spinach wilts.

In a large mixing bowl, whisk together the eggs, egg whites, Dijon mustard, fresh thyme leaves, nutmeg, milk, Greek yogurt, salt, and black pepper until well combined.

Spray a 3-quart baking dish with cooking spray. Layer one-third of the bread cubes, half of the sautéed spinach mixture, a third of the bacon, and a third of the grated cheeses. Repeat, finishing with the last layer of cheese.

Pour the whisked egg mixture evenly over the layered ingredients. Press down gently to ensure the bread is fully soaked. Cover with plastic wrap and refrigerate for at least 8 hours or overnight.

Before baking, let the strata sit at room temperature for 30 minutes and preheat the oven to 350°F (175°C).

Bake uncovered for 50 to 65 minutes, or until puffed and golden brown. Let it stand for about 5 minutes before slicing and serving.