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We also used PICRUSt to predict the functional potential of the microbiota associated with each meal in this study. Of course, this is not a perfect substitute for metagenomic sequencing or experimental studies, but it does allow one to develop some initial hypotheses related to the function of a microbial community. For example, between diet types, the most significant difference in KEGG functional categories was for “other N-glycan degradation.” This function was over-represented in the Vegan diet, which is perhaps not surprising given that cellulose is a glycan, and the Vegan diet is significantly higher in cellulose than the others. This suggests that when one consumes a diet that is high in cellulose, one also consumes a population of microbes that is well equipped to digest cellulose.   ##Caveats  It is important to point out some caveats with regard to this study. First, the scale of this study was limited. Our objective with this preliminary study was to explore the possiblity that the microbes in our food may be meaningful contributors as inputs into the ecosystem of our gut microbiota. The current paradigm is that ingested microbes are irrelevant unless they are virulent pathogens. Yet, there is no evidence that this is indeed the case. On the contrary, recent reports show that there are microbial blooms within 24 hours of large shifts in the diet \cite{Wu_2011, Walker_2011), \cite{Wu_2011}\cite{Walker_2010},  attributed to changes in the available fermentable substrate, which in turn promoted the growth of specific bacteria already present in the gut. While this is likely the case, given that it is unknown which microbes are on our food in the first place, it is not reasonable to exclude the possbility that microbes present on the food itself contributed at least in part to these observed transient blooms or shifts. Furthermore, these transient shifts in gut mcirobiota composition are currently being ignored as unimportant because the gut microbiota rebounds to its initial state following the bloom or shift. However, ecology theory tells us that perturbations to a system, however short, have the potential to disrupt a system that is not robust past the point of its ability to recover to its original state. Therefore, it is possible that under certain conditions, such perturbations could lead to functional and long-lasting changes. Nevertheless, the goal of this study was not to explore the explicit effects of ingesting food microbes on changes in the gut microbiota but simply to provide preliminary data on the composition and numbers of bacteria in typical American dietary patterns. The Second, the  studyalso  did not aim to be exhaustive in its exploration of diets. We did not aim to produce statistically significant differences in microbial composition and quantity in replicates across multiple days of a particular dietary pattern. Instead, the aim was to generate hypotheses about dietary microbes and their variation across meals and diets that could be followed up with more rigorous studies. Because the purpose of this study was to generate hypotheses rather than test specific hypotheses, multiple testing corrections were not applied in our statistical analyses.  ##Future Directions   It is possible that part of the high variation in gut microbiota composition observed among individuals is due to the specific and complex differences in diet beyond the nutrient composition that can be estimated from dietary records and recalls. This study begs the question: do the microbes we eat as part of our normal daily diets contribute to the composition and function of our gut microbiota? There are many questions that remain to be answered. Under what circumstances do microbes consumed as part of meals remain in the gastrointestinal tract transiently versus persistently following a meal? Do the microbes we eat affect the function of the resident gut microbiota, even if they do not affect its composition, as has been suggested by some yogurt feeding studies \cite{McNulty_2011}? How do different cooking and preparation methods affect the microbe composition of meals and the survival characteristics of individual microbes through the gastrointestinal tract? How do specific factors such as length of transport or provenance of individual ingredients (e.g. imported vs. domestic), packaging materials, and handling of ingredients in homes alter the microbial composition of foods? The findings of this study suggest that the microbes we eat as part of normal diets vary in absolute abundance, community composition, and function. This variation depends on the specific ingredients in the meals, whether and how the foods are prepared and processed, and other potential factors, not explored here, including the provenance of ingredients. The significance of this variation on the gut microbiota composition and function, and its impact on human health remains to be elucidated. Future studies need to explore these questions in rigorous study designs aimed at addressing key questions about the composition and content of food microbes and how these vary across diets and meals, and their impacts on the short term and long term composition and function of the gut microbiota.