Put water, bonita flakes, shiitakes, leeks, ginger, vinegar, soy sauce, and mirin in a soup pot. Bring to a boil, reduce heat, cover, and simmer for 10 minutes.
In a separate pot, boil soba noodles until al dente, about 5 minutes. Drain.
Note: Start both pots at same time.
Toast sesame seeds over medium heat in small skillet until aromatic.
Add spinach to soup pot. Turn off heat and cover.
Put miso in a ladle, fill with hot soup liquid, and press miso with spoon until miso dissolves. Mix miso liquid back into soup.
Divide soba noodles into heated bowls. Ladle soup over noodles. Garnish with green onions and sesame seeds.
Makes 2 servings.
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