This right here. It's easy to talk about optimizing gut bacteria when people aren't dying in the streets of cholera. Not saying we haven't swung too far in the other direction, but we've solved some very big problems with water treatment and hand washing.
I can't refute the statistical point, but even if it is a small minority, the ones that do have a negative effect can be catastrophic. A vanishingly small percentage of wild animal bites transmit rabies, but we still treat the bites seriously with a vaccine because the consequences of being wrong are much worse than the consequences of a false positive.
We prevent an enormous amount of death and disease, very cheaply, with hygiene.