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Fungal Infections of the Gastrointestinal Tract. The thinking about fungi has evolved from unusual agents considered contaminants and colonizers to actual pathogens. Fungi are ubiquitous in nature and are found throughout in association with food, soil, mammals, and insects. Fungi have become important pathogens in animals and humans causing infections extending from superficial disease to disseminated infection. Because the gastrointestinal tract is continually exposed to fungi, it is frequently colonized and infected by numerous yeast and other fungi. It is also the origin of many disseminated fungal infections. The increased incidence of fungal infections has led to the approval and use of novel antifungals.