Effects of a ketogenic and low-fat diet on the human metabolome, microbiome, and foodome in adults at risk for Alzheimer's disease

Abstract

Introduction: The ketogenic diet (KD) is an intriguing therapeutic candidate for Alzheimer's disease (AD) given its protective effects against metabolic dysregulation and seizures. Gut microbiota are essential for KD-mediated neuroprotection against seizures as well as modulation of bile acids, which play a major role in cholesterol metabolism. These relationships motivated our analysis of gut microbiota and metabolites related to cognitive status following a controlled KD intervention compared with a low-fat-diet intervention.

Methods: Prediabetic adults, either with mild cognitive impairment (MCI) or cognitively normal (CN), were placed on either a low-fat American Heart Association diet or high-fat modified Mediterranean KD (MMKD) for 6 weeks; then, after a 6-week washout period, they crossed over to the alternate diet. We collected stool samples for shotgun metagenomics and untargeted metabolomics at five time points to investigate individuals' microbiome and metabolome throughout the dietary interventions.

Results: Participants with MCI on the MMKD had lower levels of GABA-producing microbes Alistipes sp. CAG:514 and GABA, and higher levels of GABA-regulating microbes Akkermansia muciniphila. MCI individuals with curcumin in their diet had lower levels of bile salt hydrolase-containing microbes and an altered bile acid pool, suggesting reduced gut motility.

Discussion: Our results suggest that the MMKD may benefit adults with MCI through modulation of GABA levels and gut-transit time.

Keywords: Alzheimer's disease; ketogenic diet; low-fat American Heart Association Diet (AHAD); metabolome; microbiome; mild cognitive impairment.

Figure 1.. Microbiome (left column), food-omics (middle column), and metabolome (right column), separate by subject and by diet across time.

Robust Aitchison Principal Component Analysis (RPCA) PC1 (x-axis) and PC2 (y-axis) colored by subject identification with marker shape by diet across study, clusters by subject. Compositional tensor factorization, method accounting from repeated measures across time (x-axis) PC1 (y-axis) colored by diet types, follows crossover study design in each data modality.

Figure 2.. Microbial strains (left), foods (middle), and metabolites (right) related to cognitive status, but not necessarily diet type.

The differential abundances for the top 10 and bottom 10 with mean (bar) and model 95% confidence interval (error bars) associated with cognitive normal (more positive, blue) and mild cognitive impairment (more negative, red) (A, B, C). The log-ratio (y-axis) of the top and bottom bacterial strains (D&E) plotted across time (x-axis) and colored by cognitive status. Presented cognitive status p-values in log-ratio plots are determined from linear mixed effects models with fixed effects of diet, cognitive status, period, and diet sequences with random effect of subject.

Figure 3.. Microbial strains (left), foods (middle), and metabolites (right) related to diet type, but not necessarily cognitive status.

The differential abundances for the top 10 and bottom 10 with mean (bar) and model 95% confidence interval (error bars) associated with cognitive Ketogenic (more positive, green) and low-fat / american heart association diets (more negative, blue) (A, B, C). The log-ratio (y-axis) of the top and bottom bacterial strains (D), and sum of the top and bottom 10 foods (E) or metabolites (F) plotted across time (x-axis) and colored by diet. Presented diet stage p-values in log-ratio plots are determined from linear mixed effects models with fixed effects of diet, cognitive status, period, and diet sequences with random effect of subject.

Figure 4.. Microbial strains (left), foods (middle), and metabolites (right) related to both cognitive status and diet.

Scatter plot of log ratios of differential abundances by diet (x-axes) and cognitive status (y-axes) for microbes, with the ten most differential microbes and metabolites in both axes colored (A). Violin plot of the log-ratio of Alistepes sp. CAG: 514 to Bifidobacterium adolescentis at four different timepoints in the study (B). Scatter plot of log ratios of differential abundances by diet (x-axes) and cognitive status (y-axes) for microbes, with the ten most differential microbes and metabolites in both axes colored (C). Violin plot of the log-ratio of plant metabolites to Diarylheptanoids at four different timepoints in the study (D). In the scatterplots shown in (A) and (C), each corner corresponds to a different subpopulation: the top right corner represents microbes/metabolites associated with the MMKD and CN, the top left corner contains the microbes/metabolites correlated with the AHAD and CN, the bottom left corner shows microbes/metabolites associated with the AHAD and mild cognitive impairment, and the bottom right corner corresponds to microbes/metabolites correlated with the MMKD and MCI. These analyses allowed us to examine microbial and metabolite changes that were modulated by both diet and cognitive status.

Figure 5.. Strongest diet and cognitive status-linked differential abundances and co-occurrences linked to bile salt hydrolase (BSH) containing bacterial species, diarylheptanoids, and bile acids (BA).

The MMvec log cooccurrence probabilities (red-blue colors, colorbar) between differentially abundant and annotated metabolites (y-axis) and microbes (x-axis) colored by their association to diet (color bar top of x-axis, color legend) (A). The log-ratio of BSH containing microbes vs. those without BSH (y-axis) across diets and diarylheptanoids consumption (x-axis) (B). The log-ratio of unconjugated to conjugated BAs (y-axis) across diets and diarylheptanoids consumption (x-axis) (C). Annotations are Level II or Level III according to the Metabolomics Standards Initiative and significance was evaluated by a two-sided t-test. (50).