If many diseases do begin in the gut or are impacted by a derangement within the gut I think its going to be difficult to turn that derangement towards health in illnesses like ME/CFS or in disease states where someone has been sick for many years due to this derangement.
The gut is spectacularly complex and mine has been in a state of profound dysfunction for over twenty years now likely due to a complex of factors, fifty plus course of antibiotics which can do terrible damage to ones biome, poor nutrition in my youth, not being breast fed, and who knows what else of a hundred other different factors.
Ive found it impossible to turn my gut towards health and I have tried just about everything, every diet, FODMap, Gaps, extremely high prebiotic fiber, low fiber, low histamine, ketogenic, fasting, probiotics, fermented foods, raw milk and colostrum, every natural anti microbial, natural anti inflammatory, FMT's, and the list goes on. Its rather remarkable that I haven't been able to turn it though others do have success. But once the gut becomes deranged and imbalanced with a dysfunctional mix of bacteria, viruses parasites, inflammation, leaky gut, in many cases it can be very hard to turn .
There are no easy solutions.
Right now Im on round two of FMT's and lots of Fresh liquid colostrum. Well see..........