Do you want links to studies? I don't mind digging those up if you're actually interested. There is tons of woo surrounding the microbiome, leaky gut, and just about every other hot topic these days. There is also solid science being done around it. I don't work in the medical field, but I had to learn a great deal over several years after an adverse reaction to antibiotics kept me sick for a very long time (despite many valiant, and sometimes less than valiant, attempts by doctors to help). It was actually very frustrating to wade through all the fad products being hocked, even by doctors that should know better, and find nuanced information.

As for the really obvious, though fairly rare, dangers such as C. Diff., other resistant pathogens, SJS, and things like drug induced liver injury, I don't think anyone working in the medical field would question the reality of those.