There’s good (and bad) bacteria all over our bodies. Our skin is coated with them and needs to be coated with them. Without the good ones on our skin, bad ones take over, and then any cuts become more likely to get infected.
I’ll update later with a source reference or two. But I’m willing to bet that Wikipedia‘s “skin flora” page has good info. Im not sure of the term for the mouth’s flora though…but I have zero doubt that it exists, simply because bacteria is everywhere. And gut bacteria get there via the mouth.
Long story short, there’s no such thing as a pure human. We exist only because we are colonized by bacteria. We’re kind of like the earth in that regard. We house living organisms and they make us what we are, without them homeostasis crumbles and so do we. So, with that in mind, we should be selectively helping the good ones and killing the bad, instead of wiping them all out.
Regarding replacing the gut bacteria with suitable enzymes for digestion, that would probably be misguided. The bacteria do more than just help digestion… they also keep bad bacteria out. And furthermore, they actually affect our mental health, keeping depression at bay for instance. Whether that’s indirectly via suppressing inflammation or some more direct means, I don’t recall.
Edit: Looks like it’s a much more direct means of influence: https://news.ycombinator.com/item?id=31100533 (There doesn’t seem to be much about this here on HN already, so I’m providing a source via HN submission in hopes of generating some discussion…)