Regarding poop transplants (FMT -- fecal microbiota transplant)...
The bottom line of my following post is that a fecal transplant could be short lived so long as a person's body likes killing the "good guys".
I did not read all the referenced articles but http://thepowerofpoop.com/why-fmt-doesnt-always-work/
had the scoop on the poop! Besides checking the health of the donor and their poop I did not see anything about "donor matching" to avoid rejection. I wonder how important that would be. Trying the feces from just any healthy donor might just be too much of a crap-shoot after all the time and preparation in the protocol. The healthy donor microbiome may not even be compatible with the recipient!
Each person will support a different family of microbiomes. Depending on the season, what a person is eating, who gave them their first French kiss, what their boss is like, each person's microbiome will vary within the family that their immune system has learned to accept in the beginnings of life.
Furthermore, there may be no more "matches" since the recipients system has become very rejectful.
We can't assume that we have "bad bacteria" that we want to get of; it's a partial truth. Something may have changed in some of us that has made us unfriendly to certain good guys. I was exposed to things ranging from industrial toxins at work to viruses and bacteria from sea water in a scuba diving mishap that my body has never seen before thus possibly triggering my immune system to attack the good guys that reduce inflammation (put in its simplest terms.); the problem is not necessarily having entities that directly increase levels inflammation. I've recently read that there are considerations to recategorize AS as an auto-inflamatory disease instead of an auto-immune disease. But if the immune system is attacking bacteria that we need then I would consider that auto-immune, and a consequence is inflammation.
If my body does not "unlearn" its hatred for the good guys then I would have to take large doses of probiotics on a life-long basis. My immune system would be busy killing them, but for as long as I take the probiotics the good guys are there providing me with the benifical effect. A fecal transplant would be short lived so long as my body likes killing the good guys.
My hope is that if the triggers are removed for long enough and my body repairs itself then my immune system would have had long enough to forget its hatred for the good guys. This could be possible in rare instances but we are more likely going to need medicine.
But still... maybe the microbiome is not the problem but their byproducts are. I can not clearly bring the effects of starch into this picture.
PS: I was in remission for a period of time while taking a brand of probiotics that had single doses of 50 billion CFUs. There were many other factors that I was doing then and many of which I am doing now but are not working. I long to get those probitoics again.