The Microbes We Eat

Jenna M. Lang ( Genome Center, University of California, Davis, CA, USA
Jonathan A. Eisen ( Genome Center, Evolution and Ecology, Medical Microbiology and Immunology, University of California, Davis, Davis, CA, USA
Angela M. Zivkovic ( Department of Nutrition, University of California, Davis, CA, USA



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 \(1.3 X 10^9\) CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at \(6 X 10^6 \)and \(1.4 X 10^6\) 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 microbial approaches beyond probiotics taken as supplements - i.e., ingested as foods - are important contributors to the composition, inter-individual variation, and function of our gut microbiota.


The human gut microbiome (the total collection of microbes found in 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 2014) (Costello 2012). How to effectively shift the microbiome and restore balance is a key question for disease prevention and treatment. The gut microbiome is influenced by a number of factors including the nature of the initial colonization at birth (e.g., vaginal vs. C-section delivery), host genotype, age, and diet. As diet is a readily modifiable factor, it is an obvious target for interventions. Several studies have confirmed high inter-individual variability in the bacterial composition of the gut microbiome in healthy individuals (Brownawell 2012), (Costello 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 2011). Although the concept of enterotypes is itself controversial, diet has been shown to play a key role in determining enterotype (Wu 2011, Filippo 2010, Muegge 2011). Although the core microbiota within each person are stable over longer time scales (e.g. 5 years), community composition is highly dynamic on shorter time scales (e.g. 0–50 weeks) (Faith 2013). In fact, major shifts occur within 1 day of a significant dietary change (Wu 2011, Turnbaugh 2009). “Blooms” in specific bacterial groups were observed in response to controlled feeding of different fermentable fibers (Walker 2011). Dietary changes affect both the structure and func