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The subcellular biochemical features of a naturally occurring enteropathy in the dog associated with bacterial overgrowth have been examined. Affected animals comprised a group of 10 German Shepherd dogs with raised serum folate and reduced vitamin B12 concentrations, mild steatorrhoea, reduced xylose absorption, and normal exocrine pancreatic function. Culture of duodenal juice showed bacterial overgrowth with mixed flora, most frequently including enterococci and Escherichia coli. Examination of peroral jejunal biopsies revealed predominantly minimal histological but distinct biochemical abnormalities in the mucosa. The specific activity of alkaline phosphatase was decreased, isopycnic density gradient centrifugation showing a marked loss particularly of the brush border component of enzyme activity. In contrast, gamma-glutamyl transferase activity was enhanced in brush border fragments of slightly increased modal density, but there were no changes in the activities of the carbohydrases, zinc-resistant alpha-glucosidase, maltase, sucrase, and lactase or of the peptidase, leucyl-2-naphthylamidase. Activities of lysosomal enzymes were increased and there was evidence for enhanced lysosomal fragility and mitochondrial disruption. The activities and density gradient distributions of marker enzymes for basal-lateral membranes, endoplasmic reticulum and peroxisomes were essentially unaltered. These findings show that bacterial colonisation of the proximal small intestine may be associated with specific alterations in microvillus membrane proteins and provide biochemical evidence for intracellular damage to the enterocytes.