Host-microbiome interactions shape the metabolic effects of ketogenic diets

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Obesity and its associated metabolic diseases represent a global health crisis, affecting more than one third of US adults. Studies in humans and animal models indicate that very low-carbohydrate, high-fat ketogenic diets (KDs) promote weight loss, improve glucose tolerance, and decrease insulin resistance and intestinal inflammation. While the primary mechanisms involved are thought to be due to a shift in hepatic metabolism from carbohydrates to lipids, the role of extrahepatic cells in mediating the systemic effects of KDs remains unclear. The goal of this RO1 application (PA-19-056) is to test the hypothesis that diet-induced shifts in the host production of ketone bodies selectively inhibit the growth of gut bacteria leading to a decrease in immune cell activation and improved metabolic phenotypes. Our extensive Preliminary Results, together with the growing body of scientific literature in this area, provide strong support for the scientific premise of our hypothesis. This work is conceptually innovative as it shifts the focus from the direct impact of diet on the gut microbiota to the role of host-microbiota interactions in mediating the effects of common diets used to treat human disease. We believe that these studies are also technically innovative as we will leverage the paired genetic manipulation of the host and the gut microbiome, a general goal that remains elusive in the microbiome field for many areas of study. We will pursue the following Specific Aims: (Aim I) the use of a new transgenic mouse model to test the impact of enteric ketogenesis on the gut microbiota; (Aim II) the use of natural strain collections and transposon mutagenesis to evaluate the specificity and genetic determinants of bacterial sensitivity to ketone bodies; and (Aim III) the use of conventional and gnotobiotic mice to test the role of KD-associated bacterial immune activation in diet-induced obesity. This research plan represents a departure from the current focus of the gut microbiome field on macronutrients, expanding the scope of microbiome studies to assess the importance of host-microbiome interactions in modulating the physiological consequences of a given diet. If successful, these studies could significantly advance our long-term goal of developing microbiome-based strategies to treat metabolic disease, with an emphasis on beneficial interactions that might be harnessed to develop the prebiotics and probiotics of the future.