Response of primate gut microbiome function to increased faunivory

An evolutionary diet shift toward animal prey, which is an easily digestible source of energy, has had important consequences for primate energetics and the evolution of modern human diets. However, in addition to the direct nutritional effects of these diet shifts, indirect effects mediated through the gut microbiota may also have contributed to human metabolism and nutritional requirements. Gut microbial community composition is influenced by host diet composition, and the gut microbiota can both increase the digestibility of the host diet and affect host metabolic programming depending on its composition (De Filippo et al., 2010; Pedersen et al., 2016; Wu et al., 2011). Therefore, shifts in primate diets may have paralleled shifts in the gut microbiome that have important implications for host energetics. The proposed study will examine how an evolutionary pattern of a shift towards an animal prey diet influences the metabolic functions of the gut microbiome and describe the implications for host metabolism. To achieve this goal, we will test the relationship between increased reliance on animal prey and gut microbial community composition and function in six species of New World primates that have varying rates of insectivory or faunivory (Table 1). This project will integrate both observational and molecular dietary data with multiple measures of gut microbiome composition (16S rRNA sequencing, shotgun metagenomic sequencing) and direct measures of the function of the gut microbiome (shotgun metagenomic sequencing, metabolomics, qPCR). We hypothesize that an increased reliance on animal prey and the associated reduction in dietary fiber will incite microbial changes that result in decreased butyrate and increased acetate production, which indicates a shift in microbial energy contributions away from the gut and toward other tissues such as the brain. The following specific questions will be addressed: Question 1: How does gut microbial composition change with increased animal prey in the diet across species? H1: As the percentage of feeding and foraging time devoted to animal prey and the diversity of DNA sequences identified to animal prey from the feces increases across host species, we expect to see a decrease in the number and relative abundance of microbial taxa associated with high fiber diets (Bacteroides) and an increase in the number and relative abundance of microbial taxa associated with high fat and protein diets (Prevotella), consistent with previous results for nonhuman primates. Question 2: Are functional changes in the gut microbiome associated with increased animal prey into the diet? H2: As the percentage of feeding and foraging time devoted to animal prey and the diversity of DNA sequences identified to animal prey from the feces increases across host species, we expect to see fewer butyrate producing genes, more acetate-producing genes, and a decreased butyrate to acetate ratio in the fecal SCFA, as is expected for a dietary shift to a low fiber, high lipid, and high protein diet.