There's the idea that we and gut bugs form a symbiosis where both extract a mutual benefit. However, all gut bugs are opportunistic and will make us sick, if not outright kill us, rather than help us fight whatever opportunity allows them to do so.
As an example, take the idea of "good" gut bugs helping our immune system deal with "bad" gut bugs. The mechanism here is a continuous immune challenge from the toxic substances - cellular proteins and stuff - they release into our gut as they die off on regular basis. From this, our immune system learns to fight off those bad gut bugs better than otherwise. The problem here is that if our immune system goes down for some reason, those good gut bugs suddenly take full opportunity and begin to make us sick - they become just as bad as the other bad gut bugs. If there was genuine symbiosis, the good gut bugs would instead compensate for the immune deficiency. There is no such thing as good or bad gut bugs, they're just bugs, we're just the host, and we fight all of them continuously.
Another idea of symbiosis comes from other species that are host to way more gut bugs than we are to do something genuinely useful like digest plant matter for example. Doesn't work for humans. The organs needed for this symbiosis don't exist in humans. In species with a large cecum, we have a tiny appendix instead. In species with multiple stomachs like ruminants that also use gut bugs for part of the digestion of grasses, we have just the one stomach that uses no gut bugs for digestion in there and instead it uses peptides and bile to digest mostly animal protein and fat. Those peptides could probably break down plant protein too, but then plant protein is enclosed in plant fiber, which we can't break down in the stomach so that's a moot point. Indeed, if certain gut bugs like candida albican or H. pylori "infect" us, i.e. proliferate to a point where their presence becomes genuinely detrimental to us, they interfere with digestion rather than enhance it.
The bulk of our gut bugs are active in the colon. The idea here is that the primary function of those gut bugs is to break down waste to recover the water. Sounds good, but we can drink water directly so it's not much of a benefit. Indeed, removal of the colon in case of colon cancer doesn't seem to be that bad when it comes to water status. It's important to note that when we say waste, we mean the stuff that could not be digested by those peptides and bile, so fiber and stuff like that.
Now there's another idea that just contradicts pretty much every other idea about gut bugs. It's called the Expensive Tissue Hypothesis, that says our gut grew smaller as our brain grew larger. The only way for this to happen is to, on the one hand, increase energy density and nutrient density of the diet, and on the other hand, simplify and make highly efficient the digestion of that diet. What this means in terms of diet we're most well adapted to eat is primarily animal flesh but especially animal fat. All other ideas about fiber, resistant starch and whatnots, is merely arguing in favor of marginal, and probably imagined, benefits. We don't thrive on margins.
I skimmed the article but I get the impression it argues in favor of feeding the gut bugs with probiotics and stuf, again with this idea of symbiosis. I got a better idea. Kill'em all, good and bad, then just eat whatever diet is best for us. The bugs will return, but now we've established a clean slate where only those that are adapted to our prefered diet will make a home for themselves. In the interim, it's unlikely that we suffer much from that, except probably when we kill'am all cuz, ya know, those toxic cellular proteins and stuf that they release as they die en masse.
Another point is flora divesity, where more diversity is better and less diversity is worse. This sounds almost like that "moderation" argument. It's just as much BS. It was observed in the Bellevue all-meat trial that certain species disappeared while other species increased in number, effectively decreasing diversity, yet it was also observed that the all-meat diet produced no adverse effect and the subjects even reported a few improvements instead.
Finally, there is no lower limit to carbs, we can eat exactly none and suffer exactly no detrimental effect.
It sounds like I'm arguing off-topic in favor of eating mostly or only meat and avoiding most or all carbs, but in fact I'm illustrating the rather baseless arguments for "good" gut bugs.