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The gut microbiome has recently emerged as a critical modulator of brain function, with the so-called gut-brain axis having multiple links with a variety of neurodegenerative and mental health conditions, including Alzheimer’s Disease (AD). Various approaches for modulating the gut microbiome toward compositional and functional states that are consistent with improved cognitive health outcomes have been documented, including probiotics and prebiotics. While probiotics are live microorganisms that directly confer beneficial health effects, prebiotics are oligosaccharide and polysaccharide structures that can beneficially modulate the gut microbiome by enhancing the growth, survival, and/or function of gut microbes that in turn have beneficial effects on the human host. In this review, we discuss evidence showing the potential link between gut microbiome composition and AD onset or development, provide an overview of prebiotic types and their roles in altering gut microbial composition, discuss the effectiveness of prebiotics in regulating gut microbiome composition and microbially derived metabolites, and discuss the current evidence linking prebiotics with health outcomes related to AD in both animal models and human trials. Though there is a paucity of human clinical trials demonstrating the effectiveness of prebiotics in altering gut microbiome-mediated health outcomes in AD, current evidence highlights the potential of various prebiotic approaches for beneficially altering the gut microbiota or gut physiology by promoting the production of butyrate, indoles, and secondary bile acid profiles that further regulate gut immunity and mucosal homeostasis, which are associated with beneficial effects on the central immune system and brain functionality.

Although eggs are a nutrient dense food delivering high quality protein and micronutrients, given that eggs are also rich in cholesterol and choline, whether egg intake is contraindicated for individuals at risk for cardiovascular disease (CVD) remains controversial. In this mini review, we provide a Precision Nutrition perspective, highlighting the importance of two factors: the effect of egg cholesterol on plasma cholesterol concentrations in most people and in cholesterol hyper-absorbers, and the effect of egg choline on plasma concentrations of trimethylamine-N-oxide (TMAO), a microbe-host co-metabolite independently associated with increased CVD risk. We discuss recent evidence from intervention studies showing that in most individuals egg intake does not have a deleterious effect on plasma lipid profiles, but also highlight that some individuals are cholesterol hyper-absorbers or individuals who are not able to maintain cholesterol homeostasis by suppressing endogenous cholesterol synthesis, and that for these individuals the intake of eggs and other dietary sources of cholesterol would be contraindicated. We also discuss the complex relationship between dietary sources of choline vs. phosphatidylcholine, the gut microbiome, and plasma TMAO concentrations, highlighting the high inter-individual variability in TMAO production and gut microbiome profiles among healthy individuals and those with metabolic conditions. Precision Nutrition approaches that allow the clinician to stratify risk and improve dietary recommendations for individual patients are desirable for improving patient compliance and health outcomes. More clinical studies are needed to determine how to identify individuals at risk for CVD for whom egg intake is contraindicated vs. those for whom egg intake is not associated with negative effects on plasma lipid profiles nor plasma TMAO concentrations.

Intense recent interest in understanding how the human gut microbiome influences health has kindled a concomitant interest in linking dietary choices to microbiome variation. Diet is known to be a driver of microbiome variation, and yet the precise mechanisms by which certain dietary components modulate the microbiome, and by which the microbiome produces byproducts and secondary metabolites from dietary components, are not well-understood. Interestingly, despite the influence of diet on the gut microbiome, the majority of microbiome studies published to date contain little or no analysis of dietary intake. Although an increasing number of microbiome studies are now collecting some form of dietary data or even performing diet interventions, there are no clear standards in the microbiome field for how to collect diet data or how to design a diet-microbiome study. In this article, we review the current practices in diet-microbiome analysis and study design and make several recommendations for best practices to provoke broader discussion in the field. We recommend that microbiome studies include multiple consecutive microbiome samples per study timepoint or phase and multiple days of dietary history prior to each microbiome sample whenever feasible. We find evidence that direct effects of diet on the microbiome are likely to be observable within days, while the length of an intervention required for observing microbiome-mediated effects on the host phenotype or host biomarkers, depending on the outcome, may be much longer, on the order of weeks or months. Finally, recent studies demonstrating that diet-microbiome interactions are personalized suggest that diet-microbiome studies should either include longitudinal sampling within individuals to identify personalized responses, or should include an adequate number of participants spanning a range of microbiome types to identify generalized responses.