There's no such thing as a good gut bug. All pathogens are opportunistic. They will spread given the opportunity - a compromised immune system (however this is achieved, a cut on the skin, there we go). Once they do, the perception that any of them are good certainly doesn't hold anymore, does it.

What we eat means what they eat. However, what we eat is what we eat first and foremost. Choose a diet based on direct effect on ourselves. Gut bugs and their diversity and so forth will invariably change. Some will die off, some will remain, others will come in and settle. Incidentally, that is one aspect of going low-carb, existing gut bugs that used to feed on carbs can no longer do so, they die off, we feel it as induction flu.

But remember, we go low-carb not for them, but for ourselves. The starch and glucose and gluten has a direct effect on us, never mind the bugs. One such effect is to compromise our immune system. Do that for the first decades of our lives, before we figure it out and go low-carb. That's how it is for most of us here. How many of us have noticed fewer symptoms of flu and colds and other common infections, or just fewer instances of infection? That's what low-carb does, that's what carbs do.

Now imagine someone like me who has supressed his immune system to zero, say for a clinical trial as a test subject for an immuno-suppressant. Near-perfect health to start, whatever good gut bugs certainly aren't good anymore, they spread. I'm nobody special, this is happening to everybody who's immune system is compromised to some degree. I'm kinda lucky that they didn't spread that much before I went low-carb, health was restored quite fully then. But low-carb doesn't protect against that immuno-suppressant, it's quite a powerful drug. Accordingly, low-carb won't do much to treat those gut bugs which have spread before we went low-carb. Oh sure, low-carb certainly makes things better, but when gut bugs spread, they spread to organs and tissues that just can't handle them no matter how well we eat.

There's the idea that some organs' unique purpose is to be host to bugs. Tonsils, appendix, the colon, maybe even the skin though in a different fashion. For the appendix for example, the local immune system is extremely strong, strong enough to keep them there, to make sure they don't spread. This tells us that no other tissue is capable of doing that. Would the liver for example be able to handle that? The point here is that those special organs are perpetually infected, yet the infection doesn't spread. No such thing as a good gut bug.