Yeasts: Are some worse on your intestines than others?

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Yes - at least in terms of real world impact. Any yeast that tend to stay in suspension result in much higher ingestion rates per pint. If you are sensitive to live yeast, that is the biggest impact.
 
I don't imagine anybody has studied it rigorously enough to have a solid answer to that question. You'd need hundreds of people testing dozens of yeast strains and making detailed reports back to the lab on the size, frequency, and texture of their bowel movements, all on an otherwise-identical diet, and enough of 'em to even out any random noise introduced by different people having different dietary sensitivities.

Your best bet is probably to do as Billl suggested, and at least get a handle on the number of yeast cells in suspension by picking more flocculent strains (and probably cold-crashing and/or using finings, if you're really worried about it).
 
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