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Something (usually diet-related) causes injury to the small intestine, resulting in impaired digestion, which leads to bacterial overgrowth and other problems, resulting in further damage, and the cycle continues.
Too much coffee and eating large meals can encourage food to pass too rapidly through the gut, leading to impaired digestion and a build-up of gas, while too much fibre can cause food to ferment in the stomach, resulting in gas caused by the bacteria.