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#Introduction  The 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 \cite{Costello_2012}. \cite{Costello\_2012}.  How to effectively shift the microbiome and restore balance, with all the interrelated immune-modulating and metabolic consequences, is a key question for disease prevention. The gut microbiome is influenced by a number of factors including the nature of the initial colonization at birth (i.e. vaginal vs. C-section), host genotype, and age, however diet is emerging as a key driver of microbiome composition and function, and is a modifiable factor, making it an obvious target for intervention. The Human Microbiome Project confirmed high inter-individual variability in the bacterial composition of the gut microbiome in healthy individuals \cite{Brownawell_2012},\cite{de_Vrese_2008}. Despite this high variability at the lower taxonomic levels, enterotypes, or distinct clusters at the genus level, were described as core community compositions that are independent of age, gender, nationality, or BMI \cite{17311983}. Diet, in particular, plays a key role in determining enterotype \cite{German_2008},\cite{Zivkovic_2011}\cite{Claesson_2012}. Although the core microbiota (i.e. abundant taxa) are stable over longer time scales (e.g. 5 years), community composition is highly dynamic on shorter time scales (e.g. 0–50 weeks) \cite{Stella_2006}. In fact, major shifts occur within 1 day of a significant dietary change \cite{German_2008}\cite{Manichanh_2010}. “Blooms” in specific bacterial groups were observed in response to controlled feeding of different fermentable fibers \cite{Ubeda_2012}. Dietary changes affect both the structure and function of the gut microbiome in animals \cite{Bien_2013}, and humans under controlled feeding conditions \cite{German_2008}. Rapid shifts in microbiome composition are observed in response to change from a vegetarian to an animal based diet \cite{Claesson_2012}\cite{Stella_2006}. An ecological perspective helps to delineate the complexity and multi-layered nature of the relationships between the microbiota, the human host, and both the nutritive and non-nutritive compounds we ingest \cite{Costello_2012}. The concept of the human gut microbiome as a distinct ecosystem allows us to identify and characterize the components of the system, including its inputs and outputs. In this case, the inputs of the system include all of the various ingested compounds that can either serve as food substrates (e.g. complex sugars) or that can be metabolized by or that affect the metabolism of the microbiota (e.g. polyphenolic compounds, environmental chemicals, medications). Some of these inputs, such as the microbial food substrates (i.e. prebiotics) have been studied somewhat extensively. It has been well documented that certain sugars such as galactooligosaccharides, fructooligosaccharides, and oligosaccharides found in milk act as prebiotics that support the establishment and growth of certain commensal microbial species (2–6). Research has also documented the effects of antibiotics, and pathogens on the microbiota composition, its recovery or lack of recovery to baseline following resolution, and the various immunological and physiological effects of these (9–11).