You know my opinion on FMT for crohn's disease. The potential damage a FMT can do to crohn's disease patients is extensive due to the presence of peyer's patches and paneth cells, where stool high in bacterial load ends up entering tissue, like we have seen from the californian study that had to be halted. All FMT crohn's disease trials should have been halted after that study. Rutgeerts and follow up studies have shown that the fecal stream high in bacterial load leads to inflammation
Crohn's disease patients also have issues with tight junctions, the intestinal wall allows translocaton of bacteria deep into tissue, which is not the case in UC, the inflammation in crohn's disease is much more severe and transmural, extending deep into tissue, compared to UC.
The potential for a FMT to harm a crohn's disease patient is real, FMT in crohn's disease is now increasingly controversial and several voices in the research community have rightfully suggested halting FMT experiments in crohn's patients after the disastrous california trial where CRP, Calpotectrin and HBI showed extensive inflammation in several patients 2 days after FMT treatment (which matches Rutgeerts findings that the fecal stream will evoke an inflammatory response days after coming into contact with previously unaffected tissue).
Aministering supposedly "good" bacteria to crohn's disease patients with probiotics or other means is not feasable since the few that might be beneficial are oxygen sensitive, like Faecalibacterium prausnitzii. One can't administer this bacteria in any shape or form because it simply dies off in the presence of oxygen.
F prausnitzii counts also drop significantly when people use EN who go in remission, which again puts into question if certain bacteria are actually that beneficial as claimed.
Several types of Lactobacillus are able to halt the spread of E coli in a petri dish, but when administered to crohn's disease patients in the form of probiotics, it does not help, again, this puts into question this idea of "beneficial" bacteria for crohn's disease.
UC and C difficile are very different diseases exclusive to the colon where FMT seems to be effective. But a side-note, it is likely the bacteriophages that make the FMT effective, when you filter out the bacteria by using a 2um filter, the FMT is just as effective. The bacteriophages likely bring down the bacterial load in the colon.