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#Introductio #Introduction  Recent advances in high-throughput genomic and metagenomic analyses have paved the way to the current renaissance in the study of the intestinal microbiome and the “supraorganism” that is the result of the complex interactions of these resident microbiota together with their human host. The gut microbiome mediates many key biological functions and its imbalance, termed dysbiosis, is associated with a number of inflammatory and metabolic diseases from acute infection to inflammatory bowel disease to asthma to obesity and insulin resistance. How to effectively shift the microbiome and restore balance, with all its interrelated immune-modulating and metabolic consequences, is a key target of investigation today. (change the whole intro to have more focus on the fact that we really don’t know whether the food we eat contains microbes that affect our intestinal tract) An ecological perspective has recently been applied to solving this problem due to studies showing the unexpectedly high degree of variation in the microbiota composition among healthy individuals (1). This application of ecological theory 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.   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). Recent studies have shown that changes in diet such as a shift from a meat to a non-meat containing diet result in significant changes in the microbiota (7,8). 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).