For me it was the opposite. I now drink only high quality filter coffee, strictly black only, instead of burnt "espresso" with dairy (never had any sugar to begin with) and my gut has improved dramatically.

I have one cup in the morning and one after lunch and I'm feeling better than ever.

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Certainly your gut will feel better relatively with the best coffee you can source and a sensible brewing method. Blue Bottle + cold brew had the least impact on my gut.