There's surely some drug therapy that equates to "give them every known antibiotic, all at once, to entirely wipe out their microbiome." Presumably this is what's done before a fecal transplant, similar to how radiation is used to kill bone marrow prior to a bone marrow transplant.

(Or maybe, given that they're willing to kill everything in there, they just pump your intestines full of chlorhexidine, or some other chemical that kills like bleach but which won't get absorbed into your bloodstream?)