If you dig around the old RPF, you can find people talking about successfully cleaning up their gut with longer antibiotic courses. Yerrang mentioned gut improvement after taking a 12 week course. The Beard also talked about success in this regard after doing multiple courses.
I’ve been thinking about this myself, and one of the biggest potential problems could be yeast overgrowth. While the danger itself may be overblown, I do think this is a potential problem. The macrolides have some anti fungal effects themselves, so they could be part of a longer course. Activated Charcoal would probably also be useful. Some foods, like garlic and caprilic acid (found in coconut oil) are antifungal, and the carrot should have some anti fungal properties as well. A no starch diet, with a fair amount of fructose, should also help. And Peat talked about Flowers of Sulphur being very effective against candida, and fungus in general. I think these things would probably be very useful, without having to resort to prescription antifungals, which tend to be more problematic than the first generation antibiotics.
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