In a large skillet, heat the olive oil on medium heat and add the onion, salt and pepper. Sautee for about 10 minutes to soften the onion, but keep from browning.
Add the beef broth, thyme, and Worcestershire sauce, and continue to simmer for another 15 minutes.
While the broth is simmering, place the bread cubes on a baking sheet, drizzle lightly with olive oil and place under the broiler until lightly browned, turn and brown the reverse side of the cubes, 1 to 3 minutes.
Spoon the soup into oven proof ramekins.
Float ciabatta cubes on the soup and place sliced Gruyere cheese on top.
Place under broiler on high heat until the cheese is melted and just starts to brown, 4 to 7 minutes. Serve immediately.