As usual, you need to evaluate your doctors' incentives. Do they make more money from
1. Cutting your wife open, with all the associated hospital care or
2. Fecal transplant, for which their competition is free DIY?
As Upton Sinclair said a long time ago: It is difficult to get a man to understand something, when his salary depends upon his not understanding it.
Edit: BTW, I wish you luck with your situation. I gained familiarity because my wife had recurrent c-diff. During this episode, I saw such non-scientific quack-like behavior that I pretty much lost faith in most of the modern Medical Industrial Complex. And this was for a bacterial infection, for which the literature is accessible to anyone with a high-degree of education and a decent biology background.
The takeaway lessons from our episode was: Take matters into your own hands as much as possible. You have 24 hours a day to work on your problems, the doctor has about 20 minutes. So if you're not an expert on your particular situation, then you're pretty well screwed.