Do jalapenos effect yeast?
I have been making bagels with jalapenos. They do not always turn out as fluffy as other bagels. I have modified the water slightly to account for the extra water in the jalapenos. Could it be that the jalapenos are killing/deactivating the yeast? I was trying to look up capsaicin's effect on yeast, but the answers do not pertain to bread.
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Also, depending on the texture of the dough and how it's handled, sometimes chunks of things mixed into the dough will mechanically reduce the rise by disrupting the structure of the rising dough.