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Digesta and tissue samples were collected from the intestinal tracts of 27 pigs to determine the relationship between intestinal morphology and the utilization of nutrients from soybean flakes. Soybean flake treatments were under-, intermediate- and overprocessed (Le., 5, 20 and 60 min of autoclaving) either without extraction or with heating before or after extraction with a 55% ethanol-water mixture. Final BW was greatest (P< .001) for pigs fed soybean flakes given 20 min of heat treatment. There was a trend (P < .09) for plasma lysine concentrations to be reduced when the unextracted soybean flakes were over-processed (60 min of heat). Differences in the flow rate of DM and N through the ileum and colon reflected differences in DM and N intake, rather than differences in intestinal function. The soybean flake treatments had no effect (P > .OS) on pH of the contents of the stomach, duodenum, ileum or colon. The ethanol extraction process increased (P < .001) N digestibility of the soybean flakes, especially when the soybean flakes were underprocessed (interaction, P < .02). Villus size (area, height and perimeter length) tended to be greater in pigs fed the soybean flakes heated after extraction and(or) exposed to the intermediate level of heat treatment. Indicators of villus shape (villus area/ villus height) and proliferative activity (crypt depth and villus heigh/crypt depth) were not affected by soybean flake treatment (P > .OS). Ethanol extraction and heat treatment affected the utilization of nutrients from soybean flakes. These effects presumably were mediated through changes in villus size, nutrient digestibility and availability, rather than from changes in villus shape, conditions reflecting an allergic response.