A recent article in <Science News> describes biofilms, diverse colonies of bacteria that are (collectively) resistent to antibiotics. Since numerous antibacterial and antifungal meds have not helped John at all, and since I know a microorganism is involved, I believe there is a biofilm somewhere in John's intestines, perhaps of macroscopic proportions. I'm not the first to explore this topic. The SCD folks have talked about biofilms for decades. In this regard, I think they're on the right track, though I don't believe their diet, which permits simple sugars in high quantities, will help. (It didn't help John in any case.) But at least they're focusing in on the cause.
Read the aforementioned article, and you'll see that iron plays a pivotal role. This is something else the SCD folks have understood for decades. Perhaps this is why John reacts to his low sugar, high fiber cereal; it is fortified with iron. (I never thought about this before.) I decide to go searching, once again, for the perfect cereal. It has to be low sugar, high fiber, whole grain, no added iron, not too many artificials, and it has to taste good. "Is that all Captain, we have five days you know." [Miri]
See the March 19 2005 issue of Science News. Intestinal bacteria can coat themselves with sugar, to evade the immune system. This is normally a good thing. A simbiotic organism, which has been helping us for tens of millions of years, has surely found a way to hide from our immune system. But when that organism mutates, and becomes our enemy, we have no way to fight it. You may wonder about antibiotics, and we've tried that twice, but remember that an antibiotic never kills the entire pathogen. It attrits their numbers, and your immune system is suppose to mop up the rest. Taking enough antibiotic to kill every last bug isn't practical. So the mutated gut bacteria simply rebounds after the course is over, and then you have to deal with its cohort in crime, candida. There seems to be no answer to this problem.
This (largely unrecognized) malady can usually be prevented by eating an ancestral diet from day one, but it can rarely be cured. Some of us find a way to manage it, with diet, but it's a lifelong process. And the diet will depend on a hundred variables, so there is no one diet that will work for everyone. It's a lange lange Strasse lang.
A friend of mine, in a similar situation, is considering a <flora transplant>, kind of like rebooting Windows after it has gone hopelessly astray. I need to do some more research on this. It sounds a little extreme, but it may be the only way.
Put your evolutionary hat on and think for a moment. If bacteria are immersed in a high carb environment, created by a western diet, some may develop the ability to harm the intestines in a way that prevents us from digesting starch and complex sugars. The undigested sugars feed the bacteria, and the cycle begins anew. The bugs have found a way to open the refigerator door, and you lose! I believe this is the underlying scenario, and once the bacteria mutate and grow, it's hard to starve them out. That is precisely what the specific carbohydrate diet tries to do. You can't digest starch, so don't eat it. (Does it hurt when you do that? Then don't do that.) Eventually the bacteria and fungi starve, your intestines heal, and you can (perhaps) digest starch once again, and enjoy some fries in moderation. It makes evolutionary sense, but is it right? I don't know.