Manipulating Gut flora in vivo
I can't think of any way to start with an intestinal "blank slate", so to speak, except with antibiotics.

Perhaps it's possible to at least partially homogenize/standardize a sample group's biota with probiotics?

If it's ethics you're worried about, perhaps draw experimental subjects from a pool already being treated with antibiotics (although this, I suppose, introduces it's own biases?).