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Perhaps if a sample could be collected when healthy and frozen for long-term storage.

In my experience antibiotics were prescribed for acute symptoms that quickly worsened. I don't think they would have delayed my treatment for the hours or days needed to collect a pre-treatment sample.

Or find a way to trigger creating the positive bacteria.

Kevin rose did a podcast with https://pendulumlife.com/ that made that seem like a great path

> I wonder whether its possible to transplant the bacteria out before such a treatment and introduce them again later..

In theory yes, but there is the challenge of avoiding re-infection with the one species you're being treated to eliminate.

Is the gut usually the main target or just as byproduct getting wiped? If not then its not necessarily an issue.

The target species may not be thriving in your gut, if the location of the infection you're treating is elsewhere, but it is probably present.