Hi Linda,
I used to think that MC was caused by a gut pathogen also, and I haven't completely given up on that, but if that is the case, then it is either a bacterium (such as Mycobacterium avian subspecies paratuberculosis) that is capable of defeating conventional treatments, including faecal transplants, or it is (more likely) a virus.
Mycobacterium avian subspecies paratuberculosis (MAP) is the bacterium that causes Johne's disease (very similar to Crohn's disease) in cattle.
Whatever the case, faecal transplants simply do not work for MC. They seem to work extremely well for treating certain bacterial infections such as antibiotic-resistant C. diff, however. Several years ago 2 or 3 members here that I can recall tried to make faecal transplants work. They repeated the treatment several times, and 1 even tried many times. But to date no one has ever reported any success that lasted for longer than a few days.
The basic problem is that MC causes gut bacteria population changes, not the other way around (IOW, gut bacteria changes normally do not cause MC).
Many different triggers can cause MC, but once it is triggered, the inflammation tends to be perpetuated by food sensitivities, not by bacterial infections. It is true that gut bacteria population demographics are changed drastically when MC is active, but that's not due to pathogenic gut bacteria — it's due to the fact that MC compromises digestion, and partially-digested food attracts different types of bacteria than normally-digested food attracts.
Anytime we change our diet, our gut bacteria change to accommodate our diet. That's why primitive (hunter-gatherer) tribes have different gut bacteria profiles than people who eat a so-called "Western" diet. The bacteria species that thrive on whatever we are eating at any particular time are the ones that take over, and the ones that cannot thrive on our current diet slowly fade away. If those hunter-gatherers begin to eat a Western diet, then their gut bacteria profile will change to be more like ours. If we eat their diet then our gut bacteria profile will change to be more like theirs.
Trying to force gut bacteria to change to a population balance that does not suit our particular diet is like trying to herd cats — it's an exercise in futility because they will always return to a balance that is optimal for our particular diet (and our digestion efficiency, or lack of digestion efficiency). As our gut heals, our digestion efficiency changes and that will cause a shift in gut bacteria populations. But trying to force that same gut bacteria change before our gut heals simply will not work because that ignores the laws of nature. After our gut heals the change will come automatically, without any assistance from us or a doctor, or anyone else.
Do you see what I'm saying, or have I just confused the issue?
To add to what Gabes wrote, here are a couple of threads about unsuccessful past faecal transplant attempts from 3 to 5 years ago. As you can see, the second one tried at least 11 times. He was in remission by diet changes before he tried the transplants, but if I recall correctly, he had the idea that the transplants would allow him to eat whatever he wanted.
They didn't, of course.
Fecal gut transplant completed
Trying FMT for healing
Tex