For Roux-en-y, the intestine literally creates a "Y." The pouch is where the food goes through, but the stomach is connected a little further down. It still produces all your stomach acids and stuff. When your food comes down the intestine and reaches the "crossroad," the stomach releases these acids and finishes breaking down the food. If you're having Roux-en-y, the pouch and stomach are completely separated, but they're connected by parts of the intestine to the rest of the intestine.
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