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Fermentation of undigested carbohydrates and amino acids in the large intestine leads to the production of short-chain fatty acids (SCFAs). Clinical practice requires analytical methods capable of fast, reliable and inexpensive quantification of SCFAs. This service provides a capillary electrophoresis method to quantify acetate, propionate, butyrate and isobutyrate in human and canine feces. Benzoic acid in the background electrolyte was selected as a suitable indirect probe for indirect UV-VIS detection. The optimized method offers quantification of acetate at concentrations above 10 μM, and propionate, butyrate and isobutyrate at concentrations above 8 μM with acceptable precision, accuracy and with no significant matrix effects.