Charged metabolite biomarkers of food intake assessed via plasma metabolomics in a population-based observational study in Japan

Exhaustive Search of Dietary Intake Biomarkers as Objective Tools for Personalized Nutrimetabolomics and Precision Nutrition Implementation

OBJECTIVE

To conduct an exhaustive scoping search of existing literature, incorporating diverse bibliographic sources to elucidate the relationships between metabolite biomarkers in human fluids and dietary intake.

BACKGROUND

The search for biomarkers linked to specific dietary food intake holds immense significance for precision health and nutrition research. Using objective methods to track food consumption through metabolites offers a more accurate way to provide dietary advice and prescriptions on healthy dietary patterns by healthcare professionals. An extensive investigation was conducted on biomarkers associated with the consumption of several food groups and consumption patterns. Evidence is integrated from observational studies, systematic reviews, and meta-analyses to achieve precision nutrition and metabolism personalization.

METHODS

Tailored search strategies were applied across databases and gray literature, yielding 158 primary research articles that met strict inclusion criteria. The collected data underwent rigorous analysis using STATA and Python tools. Biomarker-food associations were categorized into 5 groups: cereals and grains, dairy products, protein-rich foods, plant-based foods, and a miscellaneous group. Specific cutoff points (≥3 or ≥4 bibliographic appearances) were established to identify reliable biomarkers indicative of dietary consumption.

RESULTS

Key metabolites in plasma, serum, and urine revealed intake from different food groups. For cereals and grains, 3-(3,5-dihydroxyphenyl) propanoic acid glucuronide and 3,5-dihydroxybenzoic acid were significant. Omega-3 fatty acids and specific amino acids showcased dairy and protein foods consumption. Nuts and seafood were linked to hypaphorine and trimethylamine N-oxide. The miscellaneous group featured compounds like theobromine, 7-methylxanthine, caffeine, quinic acid, paraxanthine, and theophylline associated with coffee intake.

CONCLUSIONS

Data collected from this research demonstrate potential for incorporating precision nutrition into clinical settings and nutritional advice based on accurate estimation of food intake. By customizing dietary recommendations based on individualized metabolic profiles, this approach could significantly improve personalized food consumption health prescriptions and support integrating multiple nutritional data.This article is part of a Nutrition Reviews special collection on Precision Nutrition.

Plasma Metabolomic Signatures of H. pylori Infection, Alcohol Drinking, Smoking, and Risk of Gastric Cancer

Circulating metabolic profiles have shown promising potential in identifying high-risk populations for various diseases, while metabolic perturbation plays an important role in gastric cancer. In this study, we conducted a cross-sectional study with 1800 participants to identify plasma metabolite signatures associated with environmental risk factors of gastric cancer. Subsequently, we evaluated the association between these signatures and gastric cancer risk in a nested case-control study involving 326 gastric cancer cases and 326 matched cancer-free controls. We conducted mediation analyses to elucidate the potential impact of metabolites on the association between environmental factors and gastric cancer. In the cross-sectional study, we identified 46 metabolites associated with Helicobacter pylori (H. pylori) infection, 365 with alcohol drinking, and 154 with smoking status. In the nested case-control study, 60 plasma metabolites, comprising 30 lipids, 15 amino acids, 6 xenobiotics, 3 nucleotides, 2 cofactors and vitamins, 2 carbohydrate, 1 energy, and 1 peptide, were associated with gastric cancer risk. A one-standard deviation increment in the H. pylori infection-related metabolomic signature was associated with an increased risk of gastric cancer (OR = 1.66, 95% CI: 1.32-2.09, p = 1.62 × 10-5). Furthermore, the effect of H. pylori infection on gastric cancer was partially mediated by the metabolomic signature (23.28%, 95% CI: 0.09-0.56) or adenine (13.69%, 95% CI: 0.05-0.31). In conclusion, we have identified metabolites associated with environmental factors and demonstrated the association between the H. pylori infection signature and gastric cancer risk. The findings provide novel insights into characterizing high-risk population for gastric cancer.

Dietary biomarkers-an update on their validity and applicability in epidemiological studies

The aim of this literature review was to identify and provide a summary update on the validity and applicability of the most promising dietary biomarkers reflecting the intake of important foods in the Western diet for application in epidemiological studies. Many dietary biomarker candidates, reflecting intake of common foods and their specific constituents, have been discovered from intervention and observational studies in humans, but few have been validated. The literature search was targeted for biomarker candidates previously reported to reflect intakes of specific food groups or components that are of major importance in health and disease. Their validity was evaluated according to 8 predefined validation criteria and adapted to epidemiological studies; we summarized the findings and listed the most promising food intake biomarkers based on the evaluation. Biomarker candidates for alcohol, cereals, coffee, dairy, fats and oils, fruits, legumes, meat, seafood, sugar, tea, and vegetables were identified. Top candidates for all categories are specific to certain foods, have defined parent compounds, and their concentrations are unaffected by nonfood determinants. The correlations of candidate dietary biomarkers with habitual food intake were moderate to strong and their reproducibility over time ranged from low to high. For many biomarker candidates, critical information regarding dose response, correlation with habitual food intake, and reproducibility over time is yet unknown. The nutritional epidemiology field will benefit from the development of novel methods to combine single biomarkers to generate biomarker panels in combination with self-reported data. The most promising dietary biomarker candidates that reflect commonly consumed foods and food components for application in epidemiological studies were identified, and research required for their full validation was summarized.

Towards nutrition with precision: unlocking biomarkers as dietary assessment tools

Precision nutrition requires precise tools to monitor dietary habits. Yet current dietary assessment instruments are subjective, limiting our understanding of the causal relationships between diet and health. Biomarkers of food intake (BFIs) hold promise to increase the objectivity and accuracy of dietary assessment, enabling adjustment for compliance and misreporting. Here, we update current concepts and provide a comprehensive overview of BFIs measured in urine and blood. We rank BFIs based on a four-level utility scale to guide selection and identify combinations of BFIs that specifically reflect complex food intakes, making them applicable as dietary instruments. We discuss the main challenges in biomarker development and illustrate key solutions for the application of BFIs in human studies, highlighting different strategies for selecting and combining BFIs to support specific study designs. Finally, we present a roadmap for BFI development and implementation to leverage current knowledge and enable precision in nutrition research.

Identifying critical age and gender-based metabolomic shifts in a Japanese population of the Tohoku Medical Megabank cohort

Understanding the physiological changes associated with aging and the associated disease risks is essential to establish biomarkers as indicators of biological aging. This study used the NMR-measured plasma metabolome to calculate age-specific metabolite indices. In doing so, the scope of the study was deliberately simplified to capture general trends and insights into age-related changes in metabolic patterns. In addition, changes in metabolite concentrations with age were examined in detail, with the period from 55-59 to 60-64 years being a period of significant metabolic change, particularly in men, and from 45-49 to 50-54 years in females. These results illustrate the different variations in metabolite concentrations by sex and provide new insights into the relationship between age and metabolic diseases.

Measuring diet by metabolomics: a 14-d controlled feeding study of weighed food intake

BACKGROUND

Metabolomics has the potential to enhance dietary assessment by revealing objective measures of many aspects of human food intake. Although metabolomics studies indicate that hundreds of metabolites are associated with dietary intake, correlations have been modest (e.g., r < 0.50), and few have been evaluated in controlled feeding studies.

OBJECTIVES

The aim of this study was to evaluate associations between metabolites and weighed food and beverage intake in a controlled feeding study of habitual diet.

METHODS

Healthy postmenopausal females from the Women's Health Initiative (N = 153) were provided with a customized 2-wk controlled diet designed to emulate their usual diet. Metabolites were measured by liquid chromatography tandem mass spectrometry in end-of-study 24-h urine and fasting serum samples (1293 urine metabolites; 1113 serum metabolites). We calculated partial Pearson correlations between these metabolites and intake of 65 food groups, beverages, and supplements during the feeding study. The threshold for significance was Bonferroni-adjusted to account for multiple testing (5.94 × 10-07 for urine metabolites; 6.91 × 10-07 for serum metabolites).

RESULTS

Significant diet-metabolite correlations were identified for 23 distinct foods, beverages, and supplements (171 distinct metabolites). Among foods, strong metabolite correlations (r ≥ 0.60) were evident for citrus (highest r = 0.80), dairy (r = 0.65), and broccoli (r = 0.63). Among beverages and supplements, strong correlations were evident for coffee (r = 0.86), alcohol (r = 0.69), multivitamins (r = 0.69), and vitamin E supplements (r = 0.65). Moderate correlations (r = 0.50-0.60) were also observed for avocado, fish, garlic, grains, onion, poultry, and black tea. Correlations were specific; each metabolite correlated with one food, beverage, or supplement, except for metabolites correlated with juice or multivitamins.

CONCLUSIONS

Metabolite levels had moderate to strong correlations with weighed intake of habitually consumed foods, beverages, and supplements. These findings exceed in magnitude those previously observed in population studies and exemplify the strong potential of metabolomics to contribute to nutrition research. The Women's Health Initiative is registered at clinicaltrials.gov as NCT00000611.

Capillary electromigration methods for food analysis and Foodomics: Advances and applications in the period March 2021 to March 2023

This work presents a revision of the main applications of capillary electromigration (CE) methods in food analysis and Foodomics. Papers that were published during the period March 2021 to March 2023 are included. The work shows the multiple CE methods that have been developed and applied to analyze different types of molecules in foods and beverages. Namely, CE methods have been applied to analyze amino acids, biogenic amines, heterocyclic amines, peptides, proteins, phenols, polyphenols, pigments, lipids, carbohydrates, vitamins, DNAs, contaminants, toxins, pesticides, additives, residues, small organic and inorganic compounds, and other minor compounds. In addition, new CE procedures to perform chiral separation and for evaluating the effects of food processing as well as the last developments of microchip CE and new applications in Foodomics will be also discussed. The new procedures of CE to investigate food quality and safety, nutritional value, storage, and bioactivity are also included in the present review work.

Microbial Diversity in African Foods and Beverages: A Systematic Assessment

This article provides a comprehensive and in-depth examination of the microbial diversity inherent in African food and beverages, with a particular emphasis on fermented products. It identifies and characterizes the dominant microorganisms, including both prokaryotes and yeasts, prevalent in these foods, and furthermore, critically analyzes the health benefits of these microbial strains, especially their probiotic properties, which could potentially improve digestion and contribute to human health. Notably, it underscores the vital role these microorganisms play in bolstering food security across Africa by enhancing and preserving food quality and safety. It also delves into the potential applications of microbial products, such as metabolites, in the food industry, suggesting their possible use in food processing and preservation. Conclusively, with a summarization of the key findings, emphasizing the importance of gaining a deep understanding of microbial diversity in African beverages and foods. Such knowledge is crucial not only in promoting food security but also in advancing public health.

Biomarkers of moderate alcohol intake and alcoholic beverages: a systematic literature review

The predominant source of alcohol in the diet is alcoholic beverages, including beer, wine, spirits and liquors, sweet wine, and ciders. Self-reported alcohol intakes are likely to be influenced by measurement error, thus affecting the accuracy and precision of currently established epidemiological associations between alcohol itself, alcoholic beverage consumption, and health or disease. Therefore, a more objective assessment of alcohol intake would be very valuable, which may be established through biomarkers of food intake (BFIs). Several direct and indirect alcohol intake biomarkers have been proposed in forensic and clinical contexts to assess recent or longer-term intakes. Protocols for performing systematic reviews in this field, as well as for assessing the validity of candidate BFIs, have been developed within the Food Biomarker Alliance (FoodBAll) project. The aim of this systematic review is to list and validate biomarkers of ethanol intake per se excluding markers of abuse, but including biomarkers related to common categories of alcoholic beverages. Validation of the proposed candidate biomarker(s) for alcohol itself and for each alcoholic beverage was done according to the published guideline for biomarker reviews. In conclusion, common biomarkers of alcohol intake, e.g., as ethyl glucuronide, ethyl sulfate, fatty acid ethyl esters, and phosphatidyl ethanol, show considerable inter-individual response, especially at low to moderate intakes, and need further development and improved validation, while BFIs for beer and wine are highly promising and may help in more accurate intake assessments for these specific beverages.

Quality Control of Targeted Plasma Lipids in a Large-Scale Cohort Study Using Liquid Chromatography-Tandem Mass Spectrometry

High-throughput metabolomics has enabled the development of large-scale cohort studies. Long-term studies require multiple batch-based measurements, which require sophisticated quality control (QC) to eliminate unexpected bias to obtain biologically meaningful quantified metabolomic profiles. Liquid chromatography-mass spectrometry was used to analyze 10,833 samples in 279 batch measurements. The quantified profile included 147 lipids including acylcarnitine, fatty acids, glucosylceramide, lactosylceramide, lysophosphatidic acid, and progesterone. Each batch included 40 samples, and 5 QC samples were measured for 10 samples of each. The quantified data from the QC samples were used to normalize the quantified profiles of the sample data. The intra- and inter-batch median coefficients of variation (CV) among the 147 lipids were 44.3% and 20.8%, respectively. After normalization, the CV values decreased by 42.0% and 14.7%, respectively. The effect of this normalization on the subsequent analyses was also evaluated. The demonstrated analyses will contribute to obtaining unbiased, quantified data for large-scale metabolomics.

Plasma Metabolite Profiles Associated with the Amount and Source of Meat and Fish Consumption and the Risk of Type 2 Diabetes

SCOPE

Consumption of meat has been associated with a higher risk of type 2 diabetes (T2D), but if plasma metabolite profiles associated with these foods reflect this relationship is unknown. The objective is to identify a metabolite signature of consumption of total meat (TM), red meat (RM), processed red meat (PRM), and fish and examine if they are associated with T2D risk.

METHODS AND RESULTS

The discovery population includes 1833 participants from the PREDIMED trial. The internal validation sample includes 1522 participants with available 1-year follow-up metabolomic data. Associations between metabolites and TM, RM, PRM, and fish are evaluated with elastic net regression. Associations between the profiles and incident T2D are estimated using Cox regressions. The profiles included 72 metabolites for TM, 69 for RM, 74 for PRM, and 66 for fish. After adjusting for T2D risk factors, only profiles of TM (Hazard Ratio (HR): 1.25, 95% CI: 1.06-1.49), RM (HR: 1.27, 95% CI: 1.07-1.52), and PRM (HR: 1.27, 95% CI: 1.07-1.51) are associated with T2D.

CONCLUSIONS

The consumption of TM, its subtypes, and fish is associated with different metabolites, some of which have been previously associated with T2D. Scores based on the identified metabolites for TM, RM, and PRM show a significant association with T2D risk.

Plasma Metabolite Response to Simple, Refined and Unrefined Carbohydrate-Enriched Diets in Older Adults-Randomized Controlled Crossover Trial

Food intake data collected using subjective tools are prone to inaccuracies and biases. An objective assessment of food intake, such as metabolomic profiling, may offer a more accurate method if unique metabolites can be identified. To explore this option, we used samples generated from a randomized and controlled cross-over trial during which participants (N = 10; 65 ± 8 year, BMI, 29.8 ± 3.2 kg/m²) consumed each of the three diets enriched in different types of carbohydrate. Plasma metabolite concentrations were measured at the end of each diet phase using gas chromatography/time-of-flight mass spectrometry and ultra-high pressure liquid chromatography/quadrupole time-of-flight tandem mass spectrometry. Participants were provided, in random order, with diets enriched in three carbohydrate types (simple carbohydrate (SC), refined carbohydrate (RC) and unrefined carbohydrate (URC)) for 4.5 weeks per phase and separated by two-week washout periods. Data were analyzed using partial least square-discrimination analysis, receiver operating characteristics (ROC curve) and hierarchical analysis. Among the known metabolites, 3-methylhistidine, phenylethylamine, cysteine, betaine and pipecolic acid were identified as biomarkers in the URC diet compared to the RC diet, and the later three metabolites were differentiated and compared to SC diet. Hierarchical analysis indicated that the plasma metabolites at the end of each diet phase were more strongly clustered by the participant than the carbohydrate type. Hence, although differences in plasma metabolite concentrations were observed after participants consumed diets differing in carbohydrate type, individual variation was a stronger predictor of plasma metabolite concentrations than dietary carbohydrate type. These findings limited the potential of metabolic profiling to address this variable.

Plasma Metabolite Profiles Following Consumption of Animal Protein and Soybean-Based Diet in Hypercholesterolemic Postmenopausal Women

Subjective reporting of food intake can be unreliable. No objective method is available to distinguish between diets differing in protein type. To address this gap, a secondary analysis of a randomized controlled cross-over feeding trial was conducted. Assessed were fasting plasma metabolite profiles and their associations with cardiometabolic risk factors (CMRFs). Hypercholesterolemic post-menopausal women (N = 11) were provided with diets containing predominantly animal protein (AP) and soy protein (SP). Untargeted metabolomics were used to determine the plasma metabolite profiles at the end of each diet phase. Concentrations of identified metabolites (N = 829) were compared using paired t-tests adjusted for false discovery rate, partial least square-discrimination analysis (PLS-DA) and receiver operating characteristics (ROC). Among the identified metabolites, 58 differed significantly between the AP and SP diets; the majority were phospholipids (n = 36), then amino acids (n = 10), xenobiotics (n = 7), vitamin/vitamin-related (n = 3) and lipids (n = 2). Of the top 10 metabolites, amino acid-derived metabolites, phospholipids and xenobiotics comprised the main categories differing due to dietary protein type. ROC curves confirmed that the top 10 metabolites were potential discriminating biomarkers for AP- and SP-rich diets. In conclusion, amino acid-derived metabolites, phosphatidylethanolamine-derived metabolites and isoflavones were identified as potential metabolite biomarkers distinguishing between dietary protein type.

A Scoping Review of the Application of Metabolomics in Nutrition Research: The Literature Survey 2000-2019

Nutrimetabolomics is an emerging field in nutrition research, and it is expected to play a significant role in deciphering the interaction between diet and health. Through the development of omics technology over the last two decades, the definition of food and nutrition has changed from sources of energy and major/micro-nutrients to an essential exposure factor that determines health risks. Furthermore, this new approach has enabled nutrition research to identify dietary biomarkers and to deepen the understanding of metabolic dynamics and the impacts on health risks. However, so far, candidate markers identified by metabolomics have not been clinically applied and more efforts should be made to validate those. To help nutrition researchers better understand the potential of its application, this scoping review outlined the historical transition, recent focuses, and future prospects of the new realm, based on trends in the number of human research articles from the early stage of 2000 to the present of 2019 by searching the Medical Literature Analysis and Retrieval System Online (MEDLINE). Among them, objective dietary assessment, metabolic profiling, and health risk prediction were positioned as three of the principal applications. The continued growth will enable nutrimetabolomics research to contribute to personalized nutrition in the future.