Bacteria in the small intestine may result in impaired absorption of nutrients. Bacteria may lead to fat malabsorption through a process called bile acid deconjugation. Carbohydrate absorption may be affected and result in carbohydrate fermentation in the intestines and gas, bloating, pain, mucus in stools, foul-smelling stools and gas, and diarrhea. According to alternative medicine practitioners, sweets and starchy foods cause the worst symptoms.