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Whole grains are a major source of dietary fibers in the human diet that provide specific nutrients to the gut microbiota and thereby plays a major role in modulating microbiota composition and increasing diversity of the gut ecosystem. A common approach of consuming whole grains is in the form of ready-to-eat extruded breakfast cereals. Studies reported herein established that extrusion conditions not only affected the physicochemical properties but also in vitro starch digestibility, β-glucan extractability and in vitro fermentation characteristics of whole grain oats. Moderate screw speed (300 rpm) led to higher slowly digestible starch (SDS) with an accompanying decrease in rapidly digestible starch (RDS). Low moisture conditions (15%) resulted in the highest resistant starch (RS) and water-extractable β-glucan (WE-BG). Extrusion moisture significantly affected WE-BG in the extrudates, with samples processed at 15% moisture (lowest) and 21% moisture (highest) having the highest concentration of WE-BG. Extrusion moisture conditions was also found to significantly affect the production of acetate, butyrate and total SCFA by the microbiota during the first 8 h of fermentation. After 24 h, samples processed at 15% moisture supported lower Bifidobacterium counts than those produced at other conditions, but had among the highest Lactobacillus counts. Besides oats, there are other whole grain cereals and their brans that have unique structural characteristics that may impart distinct effects on fermentation by the gut microbiota with subsequent effects on the host. Since dietary fiber intake has an impact on functionality of the gut microbiota, another study was conducted to establish whether the gut microbiota from individuals consuming high dietary fiber diets (G1) could metabolize the dietary fibers from grains more efficiently and produce higher concentrations of beneficial metabolites compared with donors with lower dietary fiber intakes (G2). Fecal microbiota from G1 subjects showed less decrease in diversity during fermentation and these microbiotas showed higher carbohydrate utilization and butyrate production compared with microbiota from G2 subjects. More carbohydrates were fermented from whole grains than brans. Rye induced high carbohydrate fermentability and butyrate production accompanied by low ammonia production, but only when using fecal microbiota from G1 subjects.