That's because your stomach tosses in a bunch acid to digest the butter which inactivates the salivary amylase that was helping break down the bread. The bread then passes intact and ferments in the gut while the gallbladder adds a bunch of bile to help break down the fat. The sugars in the bread result in gas and an overabundance of bacteria. In short, there's less sugar being absorbed in the intestine because the sugars in the bread are not broken into simple sugars for absorption and that may end up being worse in the long run.
So the cheese on my nachos is a good thing?
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Not “an overabundance of bacteria,” but an overabundance of Candida, which is ok if your large intestine ecology is normal, but horrible if it is also dominated by Candida.
Habitual pizza eaters lose.
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Everything is better with butter... chew yer food.