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BACKGROUND/OBJECTIVES: Consumption of whole-grain products is known to have beneficial effects on human health. The effects of whole-grain products on the intestinal microbiota and intestinal integrity have, however, only been studied limitedly. We investigate changes of the human gut microbiota composition after consumption of whole-grain (WW) or refined wheat (RW) and further study effects on gut wall integrity. SUBJECTS/METHODS: Quantitative PCR was used to determine changes in the gut bacterial composition in postmenopausal women following a 12-week energy-restricted dietary intervention with WW (N = 38) or RW (N = 34). Intestinal integrity was determined by measuring trans-epithelial resistance (TER) across a Caco-2 cell monolayer, following exposure to faecal water. RESULTS: No significant differences in microbiota composition were observed between the two dietary groups; however, the whole-grain intervention increased the relative abundance of Bifidobacterium compared to baseline, supporting a prebiotic effect of whole-grain wheat. Faecal water increased TER independent of dietary intervention, indicating that commensal bacteria produce metabolites that generally provide a positive effect on intestinal integrity. Combining microbiota composition data from the run-in period with its effect on TER revealed a tendency for a negative correlation between the relative abundance of Bifidobacterium and TER (P = 0.09). This contradicts previous findings but supports observations of increased Salmonella infection in animal models following treatment with bifidogenic prebiotics. CONCLUSIONS: The present study shows that whole-grain wheat consumption increases the abundance of bifidobacteria compared to baseline and may have indirect effects on the integrity of the intestinal wall. European Journal of Clinical Nutrition (2013) 67, 1316-1321; doi: 10.1038/ejcn.2013.207; published online 23 October 2013 Keywords: whole grain; gut microbiota; intestinal integrity; Bifidobacteria., INTRODUCTION Consumption of whole-grain products is considered to have a beneficial effect on human health, by reducing the risk of developing cardiovascular disease, obesity, type II diabetes and specific types [...]