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The entire basis of my kids' (and now my) diet is to forbid foods that feed bad bacteria. That's the whole point. It's called the Specific Carbohydrate Diet, and while it ends up being similar to Atkins and Paleo, there are key differences because if you eat even one bite of the wrong food, you've fed the bad bacteria for several days. Paleo is good for maintaining blood sugar, and it's true you might lower the overall numbers of bad bacteria by restricting their food supply, but you will never get rid of them unless you truly starve them, which means not eating certain Paleo-legal foods like sweet potatoes or maple syrup.
What's more, many pathogenic species can go into hibernation when the food disappears, and there's a well-documented phenomenon for people on SCD where suddenly they'll get sick again for a week or two, at extremely predictable 3-month intervals. The theory is that this is the maximum length of hibernation for one or more pathogens, then they wake up and start dying in large numbers, releasing toxins that give you fatigue, diarrhea, etc. But then some of the bacteria feed on their dead buddies, and hunker down for another three months. The waves of illness get less intense each time, but people have reported the cycle going predictably for years.
There are competing theories as to whether different diseases are actually caused by different (hopefully someday identifiable) species, or whether it is simply different immune system reactions to pathogens in general. But anecdotally, remission from Crohn's on SCD tends to take 1-2 years, ulcerative colitis is usually 2-3 years, autism is 3-4. Maybe that's due to the severity of the immune response that needs correcting, or maybe it's because the specific species involved take that long to die.
There was another study recently that showed that exposure to antibiotics didn't just kill a lot of the good bacteria, it fundamentally altered the metabolism of the good bacteria that survived, and they never recovered.
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