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I have been skinny until today when since I was small. Is bad bacteria damage my intestines causing irritation and reduced nutritional absorption? Can probiotics protect the GI tract and allow nutrients to be absorbed?

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and therefore gain weight?

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Small intestinal bacterial overgrowth (SIBO), which is overgrowth of otherwise beneficial bacteria in your intestine can actually cause you to loose weight. Parasites can do the same. It is very unlikely probiotics alone will help you either treat SIBO or gain weight, though.
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