Refreshing to read an honest "the more we know the more we realize how much we don't know" about gut flora (amidst so much click bait hype and supposed probiotic quick cures). My father was a large animal vet, my late wife a labor & delivery nurse, myself a water/wastewater Engineer, the basic gut flora successes have been in learning the power of mother's milk and other benefits conferred at birth, plus FMT (as you say), and perhaps "fiber is good" (Dad learned that with milk cows). I read a few years ago that we know that antibiotics work, but not really how. Apparently antibiotics favor certain flora over others, and perhaps a probiotic may even be a weak antibiotic (semantics?) It would seem that various gut flora are like people, some always good or bad, most sometimes good/sometimes bad depending on the situation, different for different people. My attempt at an explanation: https://medium.com/p/bb52d2af3d45