Preheat the oven to 375 degrees. Lightly grease 6 gratins, ramekins, or a medium size baking dish.

Add pasta to a large pot of salted boiling water and cook according to the directions until al dente. Drain well.

Meanwhile, heat the milk over low heat in a small saucepan.

In a large pot over medium-low heat, melt butter. Add onions, cook until fragrant and softened, about 2-3 minutes. Add flour, whisk until combined and golden, about 1-2 minutes.

Gradually add the hot milk and cook for 1-2 minutes more, whisking continuously until the sauce has thickened and smooth. Remove from heat and stir in Gruyere, Cheddar, salt, pepper, and nutmeg.

Add the cooked pasta and crab, stir well. Spoon the mixture into prepared individual ramekins, gratins, or a baking dish; sprinkle evenly with breadcrumbs and thyme.

Bake for 25 to 30 minutes, or until the sauce is bubbly and browned on the top.