Put the water, sake, and shijimi clams into a pot to boil.
Be careful—if the broth comes to a boil, it will really foam up and might cause the pot to overflow, so watch it carefully.
Since the bubbles (the scum) will keep on surfacing even if you skim them off consistently, turn the heat off once all the clams have opened.
When all the clams have opened, whisk in the miso to finish.
You can make miso soup with manila clams the same way.
Story Behind this Recipe
Clams produce a great broth with a lot of flavor.
You should definitely add sake since it reduces any unpleasant odor while improving the flavor as a whole. Although I usually add dashi stock into my miso soup, I don't use it for this particular recipe since the clams give out plenty of nice flavor. Still, feel free to go ahead and add some dashi stock if you'd like.