I think the short answer is, "No one really knows for sure." And not just in some sort of pedantic scientist fashion but in a real practical way. Science is just scratching the surface of this, just getting started.

We don't even have a near complete list of the bugs that are in our gut. That's important. Until we do, we can't know what is ”normal". We can speculate all we want, come up with whatever theory we want and no one can say it's wrong.

Here's my theory which no one can disprove: "They're giving them the wrong probiotics." Its not that they're bad, in fact some of them probably do help. However there are possibly some foundational bugs that support the main bugs and without those foundational buugs the main bugs die then must be replenished.

What evidence do I have? None that would stand up in court but I have noticed, um, stable gut states that go along with certain weight loss rates. This implies that there is some sort of hystorisis between stable states. Probiotics disturb the gut bio màkeup but they do not shift it to another stable state.

Maybe.