In a stockpot of boiling, salted water, cook the pasta until it is al dente. Drain the pasta and set aside.
In a sauté pan heat the olive oil over medium heat. Add the shallots and garlic and cook for 3 minutes. Add the tomatoes including all the liquid in the can, Enjuku Koji Miso, and fresh thyme leaves. Cook for 3 minutes, then reduce to a low heat. Simmer for 8 minutes; stir in olives.
Add cooked pasta into the sauce pan and toss to coat pasta well.
Divide pasta to dinner plates or bowls. Garnish with Parmesan cheese and a bit of black pepper.