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After food preparation, meals were plated on a clean plate, weighed on a digital scale (model 157W, Escali, Minneapolis, MN), and then transferred to a blender (model 5200, Vita-Mix Corporation, Cleveland, OH) and processed until completely blended (approximately 1-3 minutes). Prepared, ready to eat foods that were purchased outside the home were simply weighed in their original packaging and then transferred to the blender. 4 mL aliquots of the blended meal composite were extracted from the blender, transported on dry ice and then stored at -80°C until analysis. The following analyses were completed using these meal composite samples: 1) total aerobic bacterial plate counts, 2) total anaerobic bacterial plate counts, 3) yeast plate counts, 4) fungal plate counts, and 5) rRNA analysis for microbial ecology.   ##Diet design  Diets were designed by a nutritional biologist to deliver the average number of Calories consumed by an average American per day. The average American woman is 63 inches in height and weighs 166 pounds, and the average American man is 69 inches in height and weighs 195 pounds with an average age of 35 [link_text](http://www.cdc.gov/nchs/data/nhanes/databriefs/adultweight.pdf), [National Health and Nutrition Examination Survey](http://www.cdc.gov/nchs/data/nhanes/databriefs/adultweight.pdf),  which translates to a total daily Calorie intake range of 2,000 to 2,600 Calories per day respectively to maintain weight, as determined using the USDA MyPlate SuperTracker tool [link_text](https://www.supertracker.usda.gov/MyWeightManager.aspx. 2010). Therefore an intermediate daily Calorie intake of about 2,200 Calories was chosen as the target. Meal plans were created using the NutriHand program (Nutrihand Inc., Soraya, CA). Diet nutrient composition was calculated by the NutriHand program from reference nutrient data for individual foods using the USDA National Nutrient Database for Standard Reference [link_text](http://ndb.nal.usda.gov). Three one-day meal plans were created to be representative of three typical dietary patterns that are consumed by Americans: 1) the Average American dietary pattern (AA), which includes meat and dairy and focuses on convenience foods, 2) the USDA recommended dietary pattern (USDA), which emphasizes fresh fruits and vegetables, lean meats, whole grains and whole grain products, and dairy, and 3) the Vegan dietary pattern (VEG), which excludes all animal products. The AA meal plan totaled 2268 Calories, which consisted of 35% fat, 53% carbohydrates of which 16.6 g was fiber, and 12% protein. The USDA meal plan totaled 2260 Calories, consisting of 25% fat, 49% carbohydrates of which 45 g was fiber, and 27% protein. The VEG meal plan totaled 2264 Calories and consisted of 31% fat, 54% carbohydrates of which 52 g was fiber, and 15% protein.