Genetic and environmental influences on covariation in reproducible diet-metabolite associations

Genetic association between coffee consumption and multiple myeloma mediated by plasma metabolites: a Mendelian randomization study

Background: Multiple myeloma (MM) is a hematologic malignancy closely associated with diets and metabolic disorders, showing an increasing incidence trend. Genome-wide association studies (GWAS) contribute to exploring the causal relationships between diets, metabolites, and MM, thereby revealing biological mechanisms underlying cancer progression. Methods: This study included large-scale GWAS data for two diets, four metabolomics, and MM. The two-sample Mendelian randomization (MR) analysis was conducted to assess causalities between these dietary patterns, metabolites, and MM. The MR analysis primarily employed the inverse variance weighted (IVW) method, supported by multiple sensitivity analysis and reverse MR analysis to validate significant associations. Mediation analysis identified specific metabolites mediating the causal relationships between diets and MM. Results: Univariate MR analysis suggested that coffee consumption (ORIVW = 2.72; 95% CI: 1.21-6.10; PIVW = 0.015, P_fdr = 0.022), decaffeinated coffee consumption (ORIVW = 7.10; 95% CI: 1.33-37.87; PIVW = 0.022, P_fdr = 0.022), ground coffee consumption (ORIVW = 4.04; 95% CI: 1.25-13.02; PIVW = 0.019, P_fdr = 0.022), instant coffee consumption (ORIVW = 6.13; 95% CI: 1.95-19.34; PIVW = 0.002, P_fdr = 0.008), and coffee max liking (ORIVW = 2.94; 95% CI: 1.23-7.03; PIVW = 0.015, P_fdr = 0.035) were associated with increased MM risk. Metabolomic MR analysis identified 19 plasma metabolites, 1 blood and urine biomarker, and 4 plasma lipids with significant association with MM. Mediation analysis indicated that hippurate and cinnamoylglycine mediated 35.55% (P < 0.001) and 21.85% (P = 0.002) of the genetically predicted effect of coffee consumption on MM risk, respectively. Cinnamoylglycine contributed 12.63% (P = 0.042) to the total causal effect of ground coffee consumption on MM. Hippurate (21.43%, P < 0.001), 3-hydroxyhippurate (4.39%, P = 0.031), and cinnamoylglycine (8.79%, P = 0.010) mediated the genetically predicted impact of instant coffee consumption on MM risk. Metabolic pathway analysis suggested that glutathione metabolism significantly contributes to MM pathogenesis (P = 0.002, FDR < 0.05). Conclusions: Our findings support the adverse causal effects of various coffee consumption on MM risk, identifying hippurate, 3-hydroxyhippurate, and cinnamoylglycine as key mediators, driving the relationship potentially through the glutathione metabolism pathway.

Metabotypes are linked to uncontrolled childhood asthma, gut microbiota, and systemic inflammation

BACKGROUND

Childhood asthma has been linked to distinct metabolomic profiles.

OBJECTIVE

We sought to identify phenotypes (metabotypes) in children with moderate to severe asthma through integrative fecal and serum metabolome analysis.

METHODS

Children from the Systems Pharmacology Approach to Uncontrolled Pediatric Asthma cohort with Global Initiative for Asthma treatment step 3 or higher were recruited. Asthma control was defined by the Asthma Control Test and annual exacerbation history. Targeted metabolomic profiling of feces and serum was performed using liquid chromatography and flow injection electrospray ionization-triple quadrupole mass spectrometry. Similarity network fusion integrated fecal and serum metabolome profiles, followed by spectral clustering. Clusters were analyzed for differences in asthma characteristics, food diaries, fecal microbiota composition, and levels of serum inflammatory markers and blood cells.

RESULTS

Integrative fecal and serum metabolome analysis of 92 children with moderate to severe asthma (median age, 11.5 years, 34% female) revealed 3 metabotypes. Metabotype 1 had the lowest percentage of allergic rhinitis, with elevated serum ceramides and triglycerides. Metabotype 2 had higher odds of asthma control, the highest percentage of children with 4 or more months of breast-feeding, reduced sugar intake, lowest levels of blood neutrophils and serum inflammatory markers, and elevated serum acylcarnitines and ω-3 fatty acids. Metabotype 3 included the highest percentage of uncontrolled asthma patients, with decreased serum cholesteryl esters, phosphatidylcholines, and sphingomyelins, elevated fecal amino acids, and reduced fecal microbiota diversity.

CONCLUSIONS

Metabotypes in children with moderate to severe asthma are linked to asthma control, distinct fecal microbiota, and systemic inflammatory patterns. The findings suggest that metabotyping can be valuable in precision medicine approaches for asthma.

The association of seasonal dietary shift with fecal metabolome and microbiota in the captive Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis)

The gut microbiota can act as a buffer against changes in energy and food availability and adapt plastically to fluctuations in the host's diet. However, it is unknown how changes in the gut microbiome with the seasons impact microbial metabolism and the accessibility of nutrients to hosts. The study utilized 16S rRNA and UHPLC-MS/MS approaches to examine seasonal fecal metabolome variations in the captive Yangtze finless porpoises (YFPs) to determine if these variations are linked to nutrient intake or gut microbiome composition changes. The YFPs were mostly fed a frozen and live fish diet, with different food intakes yearly. We found that gut microbial diversity remained constant, but community structure varied seasonally. Firmicutes and Cyanobacteria were higher in winter, Actinobacteria in spring and fall, and proteobacteria in summer. The genus Paeniclostridium was significantly higher in the spring season, Romboutsia and Clostridium_sensu_stricto_13 were significantly higher in the summer, while Terrisporobacter and Macrococcus were significantly higher in the fall group. The study reported that seasonal dietary variation significantly impacted the fecal metabolome by affecting the metabolism, including energy, amino acid, carbohydrate, and nucleotide metabolism of the captive YFP. Moreover, significant correlations between metabolome and microbiome were found, and these correlations may indicate that the captive YFP has adapted to cope with dietary variations and enhance energy acquisition. These findings improve our knowledge of the link between microbiota, diet, metabolites, and the physiology of the host and suggest that gut microbial populations may adapt continuously to changes in diet.

Recent advances in applying metabolomics to uncover dietary impact on cardiometabolic health

PURPOSE OF REVIEW

Cardiometabolic diseases are a major global health concern, with diet playing a crucial role in their prevention and management. Recent advancements in the identification of metabolic signatures related to dietary patterns offer a more objective assessment of individualized dietary exposure and provide deeper insights into diet-disease associations.

RECENT FINDINGS

Recent studies have shown that distinct metabolic signatures are associated with the adherence to various dietary patterns. These signatures show even stronger associations with cardiometabolic disease incidence, independent of traditional risk factors and self-reported adherence to such dietary patterns. Emerging dietary approaches, such as sustainable diets, health outcome-focused diets, and population data-driven dietary patterns, also hold promise for improving cardiometabolic health. Additionally, metabolic signatures could offer insights into diet-disease associations in underrepresented populations, addressing genetic and lifestyle differences.

SUMMARY

Application of metabolomics provides a more precise understanding of how dietary patterns influence cardiometabolic health. Although the number of studies remains limited, and current evidence is inconsistent, the approach has significant potential for improving clinical and public health strategies. Future research should prioritize prospective studies and address population- and outcome-specific dietary needs to enable targeted interventions that optimize cardiometabolic health.

Coping with extremes: Alternations in diet, gut microbiota, and hepatic metabolic functions in a highland passerine

In wild animals, diet and gut microbiota interactions are critical moderators of metabolic functions and are highly contingent on habitat conditions. Challenged by the extreme conditions of high-altitude environments, the strategies implemented by highland animals to adjust their diet and gut microbial composition and modulate their metabolic substrates remain largely unexplored. By employing a typical human commensal species, the Eurasian tree sparrow (Passer montanus, ETS), as a model species, we studied the differences in diet, digestive tract morphology and enzyme activity, gut microbiota, and metabolic energy profiling between highland (the Qinghai-Tibet Plateau, QTP; 3230 m) and lowland (Shijiazhuang, Hebei; 80 m) populations. Our results showed that highland ETSs had enlarged digestive organs and longer small intestinal villi, while no differences in key digestive enzyme activities were observed between the two populations. The 18S rRNA sequencing results revealed that the dietary composition of highland ETSs were more animal-based and less plant-based than those of the lowland ones. Furthermore, 16S rRNA sequencing results suggested that the intestinal microbial communities were structurally segregated between populations. PICRUSt metagenome predictions further indicated that the expression patterns of microbial genes involved in material and energy metabolism, immune system and infection, and xenobiotic biodegradation were strikingly different between the two populations. Analysis of liver metabolomics revealed significant metabolic differences between highland and lowland ETSs in terms of substrate utilization, as well as distinct sex-specific alterations in glycerophospholipids. Furthermore, the interplay between diet, liver metabolism, and gut microbiota suggests a dietary shift resulting in corresponding changes in gut microbiota and metabolic functions. Our findings indicate that highland ETSs have evolved to optimize digestion and absorption, rely on more protein-rich foods, and possess gut microbiota tailored to their dietary composition, likely adaptive physiological and ecological strategies adopted to cope with extreme highland environments.

Heritability of Urinary Amines, Organic Acids, and Steroid Hormones in Children

Variation in metabolite levels reflects individual differences in genetic and environmental factors. Here, we investigated the role of these factors in urinary metabolomics data in children. We examined the effects of sex and age on 86 metabolites, as measured on three metabolomics platforms that target amines, organic acids, and steroid hormones. Next, we estimated their heritability in a twin cohort of 1300 twins (age range: 5.7–12.9 years). We observed associations between age and 50 metabolites and between sex and 21 metabolites. The monozygotic (MZ) and dizygotic (DZ) correlations for the urinary metabolites indicated a role for non-additive genetic factors for 50 amines, 13 organic acids, and 6 steroids. The average broad-sense heritability for these amines, organic acids, and steroids was 0.49 (range: 0.25–0.64), 0.50 (range: 0.33–0.62), and 0.64 (range: 0.43–0.81), respectively. For 6 amines, 7 organic acids, and 4 steroids the twin correlations indicated a role for shared environmental factors and the average narrow-sense heritability was 0.50 (range: 0.37–0.68), 0.50 (range; 0.23–0.61), and 0.47 (range: 0.32–0.70) for these amines, organic acids, and steroids. We conclude that urinary metabolites in children have substantial heritability, with similar estimates for amines and organic acids, and higher estimates for steroid hormones.

Genetically-Guided Medical Nutrition Therapy in Type 2 Diabetes Mellitus and Pre-diabetes: A Series of n-of-1 Superiority Trials

Type 2 diabetes mellitus (T2DM) is a heterogeneous metabolic disorder of multifactorial etiology that includes genetic and dietary influences. By addressing the latter, medical nutrition therapy (MNT) contributes to the management of T2DM or pre-diabetes toward achieving glycaemic control and improved insulin sensitivity. However, the clinical outcomes of MNT vary and may further benefit from personalized nutritional plans that take into consideration genetic variations associated with individual responses to macronutrients. The aim of the present series of n-of-1 trials was to assess the effects of genetically-guided vs. conventional MNT on patients with pre-diabetes or T2DM. A quasi-experimental, cross-over design was adopted in three Caucasian adult men with either diagnosis. Complete diet, bioclinical and anthropometric assessment was performed and a conventional MNT, based on the clinical practice guidelines was applied for 8 weeks. After a week of “wash-out,” a precision MNT was prescribed for an additional 8-week period, based on the genetic characteristics of each patient. Outcomes of interest included changes in body weight (BW), fasting plasma glucose (FPG), and blood pressure (BP). Collectively, the trials indicated improvements in BW, FPG, BP, and glycosylated hemoglobin (HbA1c) following the genetically-guided precision MNT intervention. Moreover, both patients with pre-diabetes experienced remission of the condition. We conclude that improved BW loss and glycemic control can be achieved in patients with pre-diabetes/T2DM, by coupling MNT to their genetic makeup, guiding optimal diet, macronutrient composition, exercise and oral nutrient supplementation in a personalized manner.

Genetic and Environmental Contributions to Variation in the Stable Urinary NMR Metabolome over Time: A Classic Twin Study

Genes, sex, age, diet, lifestyle, gut microbiome, and multiple other factors affect human metabolomic profiles. Understanding metabolomic variation is critical in human nutrition research as metabolites that are sensitive to change versus those that are more stable might be more informative for a particular study design. This study aims to identify stable metabolomic regions and determine the genetic and environmental contributions to stability. Using a classic twin design, ¹H nuclear magnetic resonance (NMR) urinary metabolomic profiles were measured in 128 twins at baseline, 1 month, and 2 months. Multivariate mixed models identified stable urinary metabolites with intraclass correlation coefficients ≥0.51. Longitudinal twin modeling measured the contribution of genetic and environmental influences to variation in the stable urinary NMR metabolome, comprising stable metabolites. The conservation of an individual’s stable urinary NMR metabolome over time was assessed by calculating conservation indices. In this study, 20% of the urinary NMR metabolome is stable over 2 months (intraclass correlation (ICC) 0.51–0.65). Common genetic and shared environmental factors contributed to variance in the stable urinary NMR metabolome over time. Using the stable metabolome, 91% of individuals had good metabolomic conservation indices ≥0.70. To conclude, this research identifies 20% of the urinary NMR metabolome as stable, improves our knowledge of the sources of metabolomic variation over time, and demonstrates the conservation of an individual’s urinary NMR metabolome.