The same data reported in Turnbaugh et al. (2009b) were further analyzed using a novel methodology described in Reshef et al. (2011) that enabled the researchers to identify and compare the strength of all possible relationships among all species-level operational taxonomic units (OTUs) across all samples. For example, one possible relationship is what the researchers called a “mutual exclusion” relationship, whereby a particular OTU is present in a microbiome only in the absence of another particular OTU. Reshef and colleagues (2011) concluded that a large proportion of the microbial species relationships could be explained by diet (i.e., conventional diet versus Western diet) as well as by sex and age. So there appear to be networks of diet-dependent microbial species.

Impact of Diet on Gut Microbiota in Other Mammals

The relationship between diet and the gut microbiota is not limited to humans and mice but extends across a wide range of mammalian species. Ley et al. (2008) reported differences in microbiome structure between omnivorous, herbivorous, and carnivorous species (among a total of 60 species, including humans). Subsequently, Muegge et al. (2011) collected data indicating that the microbial communities among these three different groups of mammals have evolved different suites of genes that allow their hosts to better process their respective diets. For example, gut microbiomes in carnivores tend to be enriched with amino acid catabolism genes.

Implications of the Association Between Diet and the Microbiome

Evidence collected by Turnbaugh and others suggests that the human ability to extract and store calories from food as fat is at least partially impacted by gut microbes. In turn, dietary choices impact the gut microbiome. This diet-microbiome interaction suggests to Turnbaugh that nutrition might be better viewed from a metagenomic perspective—one that takes into account both host and microbial genetics. It also raises questions about (1) the definition of a calorie (e.g., Do scientists need to redefine a calorie in relation to the gut microbiome?), (2) the future of personalized nutrition (e.g., Can nutritionists use knowledge of the human microbiome to design personalized diets?), and (3) next-generation medical treatments (e.g., Can medical researchers use this knowledge to design microbiome-targeted interventions?).

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