Bridging the Gap from Enterotypes to Personalized Dietary Recommendations: A Metabolomics Perspective on Microbiome Research

Abstract

Advances in high-throughput DNA sequencing have propelled research into the human microbiome and its link to metabolic health. We explore microbiome analysis methods, specifically emphasizing metabolomics, how dietary choices impact the production of microbial metabolites, providing an overview of studies examining the connection between enterotypes and diet, and thus, improvement of personalized dietary recommendations. Acetate, propionate, and butyrate constitute more than 95% of the collective pool of short-chain fatty acids. Conflicting data on acetate’s effects may result from its dynamic signaling, which can vary depending on physiological conditions and metabolic phenotypes. Human studies suggest that propionate has overall anti-obesity effects due to its well-documented chemistry, cellular signaling mechanisms, and various clinical benefits. Butyrate, similar to propionate, has the ability to reduce obesity by stimulating the release of appetite-suppressing hormones and promoting the synthesis of leptin. Tryptophan affects systemic hormone secretion, with indole stimulating the release of GLP-1, which impacts insulin secretion, appetite suppression, and gastric emptying. Bile acids, synthesized from cholesterol in the liver and subsequently modified by gut bacteria, play an essential role in the digestion and absorption of dietary fats and fat-soluble vitamins, but they also interact directly with intestinal microbiota and their metabolites. One study using statistical methods identified primarily two groupings of enterotypes Bacteroides and Ruminococcus. The Prevotella-dominated enterotype, P-type, in humans correlates with vegetarians, high-fiber and carbohydrate-rich diets, and traditional diets. Conversely, individuals who consume diets rich in animal fats and proteins, typical in Western-style diets, often exhibit the Bacteroides-dominated, B-type, enterotype. The P-type showcases efficient hydrolytic enzymes for plant fiber degradation but has limited lipid and protein fermentation capacity. Conversely, the B-type features specialized enzymes tailored for the degradation of animal-derived carbohydrates and proteins, showcasing an enhanced saccharolytic and proteolytic potential. Generally, models excel at predictions but often struggle to fully elucidate why certain substances yield varied responses. These studies provide valuable insights into the potential for personalized dietary recommendations based on enterotypes.

Current progresses and challenges for microbiome research in human health: a perspective

“…Meta-transcriptomics can be performed via short- or long- read sequencing of mRNA, usually after filtering out highly abundant ribosomal rRNA, whereas both meta-proteomics and metabolomics data are generated via mass spectrometry. Specifically, meta-transcriptomics can provide insights into the microbial genetic pathways, by quantifying the abundance of transcripts in a sample reflecting bacterial gene expression activity ( Aitmanaitė et al., 2023 ); Meta-proteomics is complementary to metagenomics and meta-transcriptomic since it reflects the activity of cellular translational and post-translational processes, by measuring the levels of all the proteins synthesized by the microbiota and the host, and, hence, providing insights into the functional role of microorganisms in host health ( Hardouin et al., 2021 ); Metabolomics allow researchers to acquire a better understanding of metabolic and biochemical processes involving the microbiota and the host, by determining the levels of all small molecules in the microenvironment ( Bartsch et al., 2023 ). An interesting application of multi-omics is described in a study on the dopamine metabolism in the marine yeast Meyerozyma guilliermondii GXDK6, by using WGS for identifying the key genes for dopamine biosynthesis, and transcriptomics as well as proteomics for showing the level of activation of the related metabolic pathway ( Sun et al., 2024 ).…”