Typically, how useful are even the best probiotics in actually changing the mucosal microbiome rather than providing only a transient effect that they cause to the large intestine?

Great question. They don’t, actually. Most of the studies I’ve seen don’t have a quantitative impact on changing the mucosal microbiome, which is why you have to keep taking them. On the other hand, prebiotics have been shown to do that because they’re basically providing food for the beneficial gut bacteria that are there.

Now, that doesn’t mean that we shouldn’t take probiotics. There are thousands, if not tens of thousands, of studies indicating [the] clinical benefit of probiotics; it just means that they don’t primarily work by quantitatively increasing the levels of probiotics, and so we’ve got to get away from thinking about it like we’re filling up the tank with probiotics kind of analogy and think about probiotics more as immune modulators. Whereas prebiotics can actually quantitatively increase the gut microbiota over time.