Yes, you are overthinking this, IMO. A person with a J-pouch will never have anything close to what is generally meant by a “healthy biome.” We don’t have colons, and that where that microbiome is supposed to live. No one has any idea what a healthy pouch microbiome consists of (heck, they barely have any idea what a healthy colon microbiome consists of). It does seem like there are certain *unhealthy* pouch microbiomes, at least in some people, and antibiotics seem to help those people. This is primitive science, but it’s much better than putting yourself through misery in service of an even-less-well-developed idea. If you get significant side effects from the antibiotic(s) that’s a whole different conversation.