Meanwhile, spray a large skillet with oil or cooking spray. Sauté onion and garlic over medium-high heat until onion begins to soften. Add mushrooms and continue cooking until they begin to brown. Add tomato, spinach, thyme, salt, and remaining black pepper. Cook and stir until spinach is wilted and any liquid has evaporated, turning heat to medium low if the vegetables are browning too quickly. Adjust seasoning.