Objectives: To characterize the microbiota profiles of patients with Hirschsprung's disease (HD), and to evaluate this in relation to postoperative bowel function and the incidence of Hirschsprung-associated enterocolitis (HAEC). Methods: All patients operated on for HD at our center between 1987–2011 were invited to answer questionnaires on bowel function and to participate in a clinical follow-up for laboratory investigations, including fecal DNA extraction, fecal calprotectin (FC), and brush border lactase (LCT) genotyping. The microbiota compositions of HD patients were compared to those of healthy controls aged 2–7 years. Results: The microbiota composition of eligible HD patients (n = 34; median age 12 (range, 3–25) years) differed from the healthy controls (n = 141), showing decreased overall microbial richness (p
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