Abstract
Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some “probiotic” health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered.We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: (1) the Average American (AMERICAN): focused on convenience foods, (2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and (3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis.Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3 × 109 CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6 × 106 and 1.4 × 106 CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG categories across the three dietary patterns and for meals clustered based on whether they were raw or cooked.Further studies are needed to determine the impact of ingested microbes on the intestinal microbiota, the extent of variation across foods, meals and diets, and the extent to which dietary microbes may impact human health. The answers to these questions will reveal whether dietary microbes, beyond probiotics taken as supplements—i.e., ingested with food—are important contributors to the composition, inter-individual variation, and function of our gut microbiota.
Highlights
The human gut microbiome mediates many key biological functions and its imbalance, termed dysbiosis, is associated with a number of inflammatory and metabolic diseases from inflammatory bowel disease to asthma to obesity and insulin resistance (Machonkin et al, 2014; Costello et al, 2012)
The AMERICAN meal plan consisted of a large Starbucks Mocha Frapuccino for breakfast, a McDonald’s Big Mac, French fries, and Coca Cola for lunch, Stouffer’s lasagna for dinner, and Oreo cookies for a snack
The USDA meal plan consisted of cereal with milk and raspberries for breakfast, an apple and yogurt for a morning snack, a turkey sandwich on whole wheat bread with salad for lunch, carrots, cottage cheese and chocolate chips for an afternoon snack, and chicken, asparagus, peas and spinach on quinoa for dinner
Summary
The human gut microbiome (the total collection of microbes found in the human gut) mediates many key biological functions and its imbalance, termed dysbiosis, is associated with a number of inflammatory and metabolic diseases from inflammatory bowel disease to asthma to obesity and insulin resistance (Machonkin et al, 2014; Costello et al, 2012). Several studies have confirmed high inter-individual variability in the bacterial composition of the gut microbiome in healthy individuals (Brownawell et al, 2012; Costello et al, 2009) Despite this high variability at the species level, enterotypes, or distinct clusters at the genus level, were described as core microbiomes that are independent of age, gender, nationality, or BMI (Arumugam et al, 2011). “Blooms” in specific bacterial groups were observed in response to controlled feeding of different fermentable fibers (Walker et al, 2011) Dietary changes affect both the structure and function of the gut microbiome in animals (Hildebrandt et al, 2009), and humans under controlled feeding conditions (Wu et al, 2011). Rapid shifts in microbiome composition are observed in response to change from a vegetarian to an animal based diet (David et al, 2013)
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