Gut microbiome-metabolome interactions during ketogenic diets of varied composition

High fat and protein (ketogenic) diets that come close to eliminating all dietary carbohydrates force the body to switch from utilizing carbohydrates to fat as its main energy source. This state known as ketosis is characterized by the production of ketone bodies such as 3-hydroxybutyrate (BHB) and has been associated with weight loss, insulin resistance, mitochondria efficiency, and reduced inflammation. For example, recent evidence has suggested that alterations in the gut microbiome by ketogenic diets may play a role in improving colitis and epileptic symptoms through altered microbial metabolism of various metabolites including short chain fatty acids. However, the extent to which microbes contribute to altered host metabolism remains unclear.
To better understand this association we conducted a randomized cross-over study examining two ketogenic diets (one fat-based and one protein-based) and their impact on the gut microbiome composition and fecal and serum metabolomes of canines. Over the span of 15 weeks, healthy dogs (n=35) were fed a series of three different diets varying in fat and protein sources (5 weeks each). All dogs started on the base feed, which is a high carbohydrate standard dog food (25/37/38% percent protein/fat/carbohydrates). Then they were randomly allocated to either a high protein diet (53/39/8%) or a high-fat diet (27/68/5%) for 5 weeks. Dogs were then switched to the opposite diet for the final 5 weeks of the study. Stool samples collected at the end of each 5-week time point were used for shotgun metagenomic sequencing (MGX) and fecal metabolome profiling. Paired blood samples were also collected and subjected to metabolome profiling.
We observed strong associations between diet and overall fecal and serum chemical composition as well as gut microbiome composition (PERMANOVA p < 0.05). Similar to previous literature, we found several species of bifidobacteria such as B. criceti and B. pseudolongum to be negatively associated with both ketogenic diets (q < 0.05). Although we also noted multiple other species within the Actinobacteria phyla such as C. tanakaei, to be more abundant during ketogenic diets. Firmicutes species overall were also broadly more abundant during ketogenic diets including poorly characterized Peptostreptococcaceae and Lachnospiraceace species, a result that contrasts with previous work in humans.
Interestingly, the serum ketogenic marker 3-hydroxybutyrate (BHB) was elevated after the ketogenic fat diet (p < 0.001) but was unchanged after the ketogenic protein diet (p=0.297). Both ketogenic diets led to reduced BHB fecal concentrations (p < 0.001). In association with serum BHB levels, community abundances shifted for several gut microbes including an unclassified Eggerthellaceae species. These microbial associations reveal interesting candidates that may play roles in ketogenesis or in regulating serum metabolite profiles outside of the colon. Overall, our current results suggest that ketogenic diets alter gut microbiome communities and lead to shifts in metabolite profiles locally in feces and systemically via serum.