Jenna M. Lang edited Introduction.md  over 9 years ago

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Yet, little is known about the effects of ingested microorganisms on gut microbiota composition or function, 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. Conversely, we do know much about the microbial ecology of various specialty foods where fermentation, colonization, ripening, and/or aging are part of the preparation of these foods, for example pancetta \cite{Busconi_2014} and of course cheese \cite{Gatti_2008}. The microbial ecology of the surfaces of raw plant-derived foods such as fruits and vegetables has also been characterized \cite{23544058}. There is a large base of literature on food-borne pathogens \cite{Aboutaleb_2014}. Furthermore, it is known that the microbial ecology of endemic microbes found on food surfaces can affect mechanisms by which pathogens colonize these foods \cite{Critzer_2010}. A recent article showed that certain ingested microbes found in foods such as cheese and deli meats were detected in the stool of individuals who consumed them, and that furthermore they were culturable and thus survived transit through the upper intestinal tract \cite{David_2013}. However, the microbial ecology of different meals and diets, as well as the total number of live microorganisms ingested in these meals and diets are largely unknown.   We hypothesized that the microbes we eat vary both quantitatively and compositionally in a significant way according to dietary pattern. We have selected to characterize the microbiota of three different dietary patterns in order to determine the average total amount of daily microbes ingested via food and beverages and their composition in the average American adult across three different dietary patterns: 1) the Average American dietary pattern (AA) (AMERICAN)  focused on convenience foods, 2) the USDA recommended dietary pattern (USDA) emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and 3) the Vegan (VEG) (VEGAN)  dietary pattern, which excludes all animal products. Here we used DNA sequencing, plate counting, and informatics methods to characterize microbes in these dietary patterns.