Make the dashi (broth): In a medium saucepan over medium-high heat, bring the water and kombu to a boil. Remove the pan from heat and add the bonito flakes. Cover the pan and allow to steep for 5 minutes.

Strain stock through a fine mesh sieve or a cheesecloth-lined colander into a large bowl or another saucepan. If you are not using the stock immediately, allow to cool uncovered and then refrigerate it, covered for up to a week.

Transfer all but ½ cup of stock back to the original saucepan and add tofu and wakame, if using, and heat until hot.

Whisk miso into the reserved ½ cup of stock until smooth. If you think you will consume all of the soup now, stir all of the miso mixture to the heated stock and serve immediately. Otherwise, add a spoonful of the miso mixture to each individual bowl and ladle hot stock on top. You can add noodles to each individual bowl, if you like.