Heat the oil in a pot. Sauté onions for 5 minutes, until translucent. Remove stems from the shiitake, discard stems, reserve soaking water and slice caps thin. Add shiitake, shiitake soaking water, kombu, water and bonito flakes to the pot. Cover and bring to a boil. Reduce the flame to medium-low and simmer for 25 minutes. Reduce the flame to low, add the miso and simmer, with out boiling, for another 2 minutes.
While the soup is cooking, dry roast the bread cubes in a skillet until golden. Garnish the soup with croutons and scallions.
Per serving - 105 calories, 3 g fat (20% calories from fat), 4 g protein, 18 g carbohydrate, 4 g fiber, 0 mg cholesterol, 399 mg sodium