I think we underestimate the extent to which pathogens thrive in niches carved out by the absence of symbiotic bacteria required by our microbiomes.
Fecal transplants have shown significant results in some diseases (such as Crohn's): https://academic.oup.com/ibdjournal/article/21/3/556/4602907
> Based on [Pediatric Crohn's Disease Activity Index], 7 of 9 patients were in remission at 2 weeks and 5 of 9 patients who did not receive additional medical therapy were in remission at 6 and 12 weeks.
> No or modest improvement was seen in patients who did not engraft or whose microbiome was most similar to their donor.
So I think it's either a case of pathogens that fit in with the established microbiome or that the microbiome is missing vital components.