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1.
Curr Dev Nutr ; 6(4): nzac031, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35434472

ABSTRACT

The rapid development of nutrition science is embracing digital transformation to generate large amounts of data. Precision nutrition and "Big Data" place increasing demand for data repositories and visualization, which enhances the digital transformation. We defined the need for an integrated nutrition data platform as a web-based platform that can collect, store, track, analyze, monitor, and visually display key metrics in nutrition and health while allowing users to interact with visuals and download data provided in the platform. Interactive dashboards create new opportunities for scholars and practitioners to generate and test hypotheses. We present the development and implementation of the Global Nutrition and Health Atlas (GNHA; https://sites.tufts.edu/gnha/), an open-access online platform covering nutrition and health data with 26 themes and 500+ indicators from 190+ countries up to 30 y. We view GNHA as an interactive tool aiming to share information and perspectives and foster collaborations and innovations.

2.
Adv Nutr ; 13(3): 748-757, 2022 06 01.
Article in English | MEDLINE | ID: mdl-35254406

ABSTRACT

The rapid expansion of food and nutrition information requires new ways of data sharing and dissemination. Interactive platforms integrating data portals and visualization dashboards have been effectively utilized to describe, monitor, and track information related to food and nutrition; however, a comprehensive evaluation of emerging interactive systems is lacking. We conducted a systematic review on publicly available dashboards using a set of 48 evaluation metrics for data integrity, completeness, granularity, visualization quality, and interactivity based on 4 major principles: evidence, efficiency, emphasis, and ethics. We evaluated 13 dashboards, summarized their characteristics, strengths, and limitations, and provided guidelines for developing nutrition dashboards. We applied mixed effects models to summarize evaluation results adjusted for interrater variability. The proposed metrics and evaluation principles help to improve data standardization and harmonization, dashboard performance and usability, broaden information and knowledge sharing among researchers, practitioners, and decision makers in the field of food and nutrition, and accelerate data literacy and communication.

3.
Int J Food Sci Nutr ; 72(2): 236-247, 2021 Mar.
Article in English | MEDLINE | ID: mdl-32631124

ABSTRACT

This study evaluated the validity of nutrient and food group intakes estimated by an FFQ against biomarkers. A 71-item semiquantitative FFQ was administered to 210 Brazilian children and adolescents aged 9-13 years. Intakes were correlated with biomarkers in plasma and red blood cells. Correlations between nutrients and their biomarkers were presented for animal protein, myristic acid (C14:0), EPA, DHA, ß-carotene, folate, and vitamins B3, B5 and B6. Food groups and biomarkers were correlated as follows: fish products with EPA and DHA; milk and dairy with C14:0, pyridoxal 5'-phosphate and vitamin B12; total vegetables and dark green and orange vegetables with ß-carotene; 5-methyltetrahydrofolate with green vegetables; and flour products with para-aminobenzoylglutamic acid. This FFQ is a valid tool for ranking Brazilian children and adolescents according to their intake of several nutrients and food groups.


Subject(s)
Biomarkers/blood , Diet Surveys , Adolescent , Brazil , Child , Female , Folic Acid/blood , Humans , Male , Surveys and Questionnaires , Vitamins/blood , beta Carotene/blood
4.
Bioinformatics ; 36(9): 2943-2945, 2020 05 01.
Article in English | MEDLINE | ID: mdl-31930381

ABSTRACT

SUMMARY: Nuclear magnetic resonance (NMR)-based metabolomics is widely used to obtain metabolic fingerprints of biological systems. While targeted workflows require previous knowledge of metabolites, prior to statistical analysis, untargeted approaches remain a challenge. Computational tools dealing with fully untargeted NMR-based metabolomics are still scarce or not user-friendly. Therefore, we developed AlpsNMR (Automated spectraL Processing System for NMR), an R package that provides automated and efficient signal processing for untargeted NMR metabolomics. AlpsNMR includes spectra loading, metadata handling, automated outlier detection, spectra alignment and peak-picking, integration and normalization. The resulting output can be used for further statistical analysis. AlpsNMR proved effective in detecting metabolite changes in a test case. The tool allows less experienced users to easily implement this workflow from spectra to a ready-to-use dataset in their routines. AVAILABILITY AND IMPLEMENTATION: The AlpsNMR R package and tutorial is freely available to download from http://github.com/sipss/AlpsNMR under the MIT license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Metabolomics , Software , Magnetic Resonance Imaging , Magnetic Resonance Spectroscopy , Workflow
5.
Nutrients ; 11(9)2019 Sep 12.
Article in English | MEDLINE | ID: mdl-31547317

ABSTRACT

Previous studies have shown that the dietary diversity of young Filipino children to be limited and that the prevalence of nutrient inadequacies is high. This study extends the current knowledge to examine the relationship between diet diversity and the probability of adequacy of micronutrients among Filipino schoolchildren (aged 6 to 12 years), by the wealth status and dwelling location. The dietary intake data were collected using a single 24-h recall from 6460 children in the Filipino National Nutrition Survey 2013. The diet diversity score (DDS) and the probability of adequacies (PA) of 11 micronutrients were calculated, and further stratified by socio-economic status (SES) and dwelling location. The diet diversity was generally low (mean DDS = 4 out of 9). Children from the lowest SES, and living in rural areas, tended to have a lower DDS. Children with a DDS of 1 were likely to be inadequate in all 11 micronutrients. The higher DDS (≥6) was associated with higher PAs for the B vitamins but not for calcium, folate, iron, vitamin A and to large extent, vitamin C. This suggests that it was difficult for this population to achieve adequacy in these 5 micronutrients. More rigorous research on the topic is needed. Better access to nutrient-rich or fortified staple foods, in tandem with increased education on the importance of dietary diversity, are potential strategies to support children in achieving adequate micronutrient intakes.


Subject(s)
Diet, Healthy/statistics & numerical data , Micronutrients/analysis , Child , Child Nutrition Disorders/epidemiology , Diet, Healthy/ethnology , Female , Humans , Male , Micronutrients/deficiency , Nutrition Surveys , Nutritional Status , Philippines/epidemiology , Rural Population/statistics & numerical data , Social Class , Vitamins/analysis
6.
Mol Nutr Food Res ; 62(22): e1800396, 2018 11.
Article in English | MEDLINE | ID: mdl-30113130

ABSTRACT

SCOPE: Quinic acid in its free form is broadly abundant in plants, and can accumulate in copious amounts in coffee, tea, and certain fruits. However, it has been mostly studied as chlorogenic acid, an ester of caffeic and quinic acids. When chlorogenic acid reaches the colon, it is hydrolyzed by microbial esterases releasing caffeic and quinic acids. While biotransformation of chlorogenic and caffeic acids have been elucidated by in vitro and in vivo studies, the gut metabolism of quinic acid has been so far overlooked. METHODS AND RESULTS: [U-13 C]-Quinic acid is submitted to a colonic model using human fecal microbiota for assessing its metabolic fate. The metabolite profiles formed along microbial biotransformation are monitored by a combined metabolomics approach, using both 2D GC- and ultra-HPLC-MS. Six metabolic intermediates are identified by incorporation of isotopic label. CONCLUSION: Two parallel degradation pathways could be proposed: (1) an oxidative route, leading to aromatization and accumulation of protocatechuic acid, and a (2) reductive route, including dehydroxylation to cyclohexane carboxylic acid. Elucidating the biotransformation of food bioactives by the gut microbiota is of relevance for understanding nutrition, interindividual variability and potential effects on human metabolism.


Subject(s)
Gastrointestinal Microbiome/physiology , Quinic Acid/pharmacokinetics , Carbon Isotopes/pharmacokinetics , Chlorogenic Acid/metabolism , Chlorogenic Acid/pharmacokinetics , Feces/microbiology , Gas Chromatography-Mass Spectrometry , Humans , Quinic Acid/metabolism
7.
Nutrients ; 10(2)2018 Jan 30.
Article in English | MEDLINE | ID: mdl-29385742

ABSTRACT

The Brazilian Healthy Eating Index-Revised (BHEI-R) can be used to determine overall dietary patterns. We assessed the BHEI-R scores in children and adolescents, aged from 9 to 13 years old, and associated its component scores with biomarkers of health and dietary exposure. Three 24-h recalls were used to generate BHEI-R. Biomarkers were analyzed in plasma and red blood cells. Correlation tests, agreement, and covariance analyses were used to associate BHEI-R components with biomarkers. Data from 167 subjects were used. The strongest correlations were between fruits, vegetables and legumes with omega-6 and omega-3 fatty acids, and ß-carotene intakes. Milk and dairy correlated with plasma retinol and pyridoxine. All components rich in vegetable and animal protein sources correlated with plasma creatine. Total BHEI-R scores were positively associated with intakes of omega-6, omega-3, fiber and vitamin C, and inversely associated with energy and saturated fat intakes of individuals. Plasma ß-carotene and riboflavin biomarkers were positively associated with total BHEI-R. An inadequate food consumption pattern was captured by both biomarkers of health and dietary exposure. BHEI-R was validated for the above dietary components and can be associated with metabolomics and nutritional epidemiological data in future pediatric studies.


Subject(s)
Adolescent Nutritional Physiological Phenomena , Child Nutritional Physiological Phenomena , Diet, Healthy , Nutrition Assessment , Patient Compliance , Adolescent , Adolescent Nutritional Physiological Phenomena/ethnology , Biomarkers/blood , Biomarkers/metabolism , Brazil , Child , Child Nutritional Physiological Phenomena/ethnology , Diet, Healthy/ethnology , Erythrocytes/metabolism , Fabaceae/chemistry , Fatty Acids, Omega-3/administration & dosage , Fatty Acids, Omega-3/blood , Fatty Acids, Omega-3/metabolism , Fatty Acids, Omega-6/administration & dosage , Fatty Acids, Omega-6/blood , Fatty Acids, Omega-6/metabolism , Fruit/chemistry , Humans , Longitudinal Studies , Nutritive Value , Patient Compliance/ethnology , Riboflavin/administration & dosage , Riboflavin/blood , Riboflavin/metabolism , Seeds/chemistry , Self Report , Vegetables/chemistry , beta Carotene/administration & dosage , beta Carotene/blood , beta Carotene/metabolism
8.
Sci Rep ; 8(1): 1393, 2018 01 23.
Article in English | MEDLINE | ID: mdl-29362412

ABSTRACT

In longitudinal clinical studies, methodologies available for the analysis of multivariate data with multivariate methods are relatively limited. Here, we present Consensus Clustering (CClust) a new computational method based on clustering of time profiles and posterior identification of correlation between clusters and predictors. Subjects are first clustered in groups according to a response variable temporal profile, using a robust consensus-based strategy. To discover which of the remaining variables are associated with the resulting groups, a non-parametric hypothesis test is performed between groups at every time point, and then the results are aggregated according to the Fisher method. Our approach is tested through its application to the EarlyBird cohort database, which contains temporal variations of clinical, metabolic, and anthropometric profiles in a population of 150 children followed-up annually from age 5 to age 16. Our results show that our consensus-based method is able to overcome the problem of the approach-dependent results produced by current clustering algorithms, producing groups defined according to Insulin Resistance (IR) and biological age (Tanner Score). Moreover, it provides meaningful biological results confirmed by hypothesis testing with most of the main clinical variables. These results position CClust as a valid alternative for the analysis of multivariate longitudinal data.


Subject(s)
Insulin Resistance , Prediabetic State/metabolism , Adolescent , Algorithms , Body Weights and Measures , Child , Child, Preschool , Cluster Analysis , Consensus , Female , Humans , Longitudinal Studies
9.
Front Physiol ; 9: 1903, 2018.
Article in English | MEDLINE | ID: mdl-30733683

ABSTRACT

Aging is a dynamic process depending on intrinsic and extrinsic factors and its evolution is a continuum of transitions, involving multifaceted processes at multiple levels. It is recognized that frailty and sarcopenia are shared by the major age-related diseases thus contributing to elderly morbidity and mortality. Pre-frailty is still not well understood but it has been associated with global imbalance in several physiological systems, including inflammation, and in nutrition. Due to the complex phenotypes and underlying pathophysiology, the need for robust and multidimensional biomarkers is essential to move toward more personalized care. The objective of the present study was to better characterize the complexity of pre-frailty phenotype using untargeted metabolomics, in order to identify specific biomarkers, and study their stability over time. The approach was based on the NU-AGE project (clinicaltrials.gov, NCT01754012) that regrouped 1,250 free-living elderly people (65-79 y.o., men and women), free of major diseases, recruited within five European centers. Half of the volunteers were randomly assigned to an intervention group (1-year Mediterranean type diet). Presence of frailty was assessed by the criteria proposed by Fried et al. (2001). In this study, a sub-cohort consisting in 212 subjects (pre-frail and non-frail) from the Italian and Polish centers were selected for untargeted serum metabolomics at T0 (baseline) and T1 (follow-up). Univariate statistical analyses were performed to identify discriminant metabolites regarding pre-frailty status. Predictive models were then built using linear logistic regression and ROC curve analyses were used to evaluate multivariate models. Metabolomics enabled to discriminate sub-phenotypes of pre-frailty both at the gender level and depending on the pre-frailty progression and reversibility. The best resulting models included four different metabolites for each gender. They showed very good prediction capacity with AUCs of 0.93 (95% CI = 0.87-1) and 0.94 (95% CI = 0.87-1) for men and women, respectively. Additionally, early and/or predictive markers of pre-frailty were identified for both genders and the gender specific models showed also good performance (three metabolites; AUC = 0.82; 95% CI = 0.72-0.93) for men and very good for women (three metabolites; AUC = 0.92; 95% CI = 0.86-0.99). These results open the door, through multivariate strategies, to a possibility of monitoring the disease progression over time at a very early stage.

10.
Cell Rep ; 20(7): 1729-1743, 2017 08 15.
Article in English | MEDLINE | ID: mdl-28813682

ABSTRACT

Lysine acetylation is involved in various biological processes and is considered a key reversible post-translational modification in the regulation of gene expression, enzyme activity, and subcellular localization. This post-translational modification is therefore highly relevant in the context of circadian biology, but its characterization on the proteome-wide scale and its circadian clock dependence are still poorly described. Here, we provide a comprehensive and rhythmic acetylome map of the mouse liver. Rhythmic acetylated proteins showed subcellular localization-specific phases that correlated with the related metabolites in the regulated pathways. Mitochondrial proteins were over-represented among the rhythmically acetylated proteins and were highly correlated with SIRT3-dependent deacetylation. SIRT3 activity being nicotinamide adenine dinucleotide (NAD)+ level-dependent, we show that NAD+ is orchestrated by both feeding rhythms and the circadian clock through the NAD+ salvage pathway but also via the nicotinamide riboside pathway. Hence, the diurnal acetylome relies on a functional circadian clock and affects important diurnal metabolic pathways in the mouse liver.


Subject(s)
Circadian Clocks/physiology , Circadian Rhythm/physiology , Liver/enzymology , Mitochondrial Proteins/metabolism , Protein Processing, Post-Translational , Proteome/metabolism , ARNTL Transcription Factors/deficiency , ARNTL Transcription Factors/genetics , Acetylation , Animals , Cryptochromes/deficiency , Cryptochromes/genetics , Eating/physiology , Lysine , Metabolic Networks and Pathways/physiology , Mice , Mice, Inbred C57BL , Mice, Knockout , Mitochondrial Proteins/genetics , NAD/metabolism , Photoperiod , Proteome/genetics , Sirtuin 3/genetics , Sirtuin 3/metabolism
11.
Alzheimers Res Ther ; 9(1): 43, 2017 Jun 17.
Article in English | MEDLINE | ID: mdl-28623948

ABSTRACT

BACKGROUND: Hyperhomocysteinemia is a risk factor for cognitive decline and dementia, including Alzheimer disease (AD). Homocysteine (Hcy) is a sulfur-containing amino acid and metabolite of the methionine pathway. The interrelated methionine, purine, and thymidylate cycles constitute the one-carbon metabolism that plays a critical role in the synthesis of DNA, neurotransmitters, phospholipids, and myelin. In this study, we tested the hypothesis that one-carbon metabolites beyond Hcy are relevant to cognitive function and cerebrospinal fluid (CSF) measures of AD pathology in older adults. METHODS: Cross-sectional analysis was performed on matched CSF and plasma collected from 120 older community-dwelling adults with (n = 72) or without (n = 48) cognitive impairment. Liquid chromatography-mass spectrometry was performed to quantify one-carbon metabolites and their cofactors. Least absolute shrinkage and selection operator (LASSO) regression was initially applied to clinical and biomarker measures that generate the highest diagnostic accuracy of a priori-defined cognitive impairment (Clinical Dementia Rating-based) and AD pathology (i.e., CSF tau phosphorylated at threonine 181 [p-tau181]/ß-Amyloid 1-42 peptide chain [Aß1-42] >0.0779) to establish a reference benchmark. Two other LASSO-determined models were generated that included the one-carbon metabolites in CSF and then plasma. Correlations of CSF and plasma one-carbon metabolites with CSF amyloid and tau were explored. LASSO-determined models were stratified by apolipoprotein E (APOE) ε4 carrier status. RESULTS: The diagnostic accuracy of cognitive impairment for the reference model was 80.8% and included age, years of education, Aß1-42, tau, and p-tau181. A model including CSF cystathionine, methionine, S-adenosyl-L-homocysteine (SAH), S-adenosylmethionine (SAM), serine, cysteine, and 5-methyltetrahydrofolate (5-MTHF) improved the diagnostic accuracy to 87.4%. A second model derived from plasma included cystathionine, glycine, methionine, SAH, SAM, serine, cysteine, and Hcy and reached a diagnostic accuracy of 87.5%. CSF SAH and 5-MTHF were associated with CSF tau and p-tau181. Plasma one-carbon metabolites were able to diagnose subjects with a positive CSF profile of AD pathology in APOE ε4 carriers. CONCLUSIONS: We observed significant improvements in the prediction of cognitive impairment by adding one-carbon metabolites. This is partially explained by associations with CSF tau and p-tau181, suggesting a role for one-carbon metabolism in the aggregation of tau and neuronal injury. These metabolites may be particularly critical in APOE ε4 carriers.


Subject(s)
Alzheimer Disease/cerebrospinal fluid , Alzheimer Disease/epidemiology , Carbon Compounds, Inorganic/cerebrospinal fluid , Carbon/blood , Cognition Disorders/cerebrospinal fluid , Cognition Disorders/epidemiology , Homocysteine/cerebrospinal fluid , Aged , Alzheimer Disease/diagnosis , Biomarkers/blood , Biomarkers/cerebrospinal fluid , Cognition Disorders/diagnosis , Comorbidity , Female , Humans , Male , Prevalence , Risk Factors , Switzerland/epidemiology
12.
J Nutr Biochem ; 43: 98-106, 2017 05.
Article in English | MEDLINE | ID: mdl-28282585

ABSTRACT

Polyunsaturated fatty acids (PUFA) contained in fish oil (FO) are ligands for peroxisome proliferator-activated receptors (PPAR) that may induce changes in cardiometabolic markers. Variation in PPAR genes may influence the beneficial responses linked to FO supplementation in young adults. The study aimed to analyze the effect of FO supplementation on glucose metabolism, circulating lipids and inflammation according to PPARα L162V and PPARγ2 P12A genotypes in young Mexican adults. 191 young, non-smoking subjects between 18 and 40 years were included in a one-arm study. Participants were supplemented with 2.7 g/day of EPA+DHA, during six weeks. Dietary analysis, body composition measurements and indicators for glucose metabolism, circulating lipids, and markers for inflammation were analyzed before and after intervention. An overall decrease in triglycerides (TG) and an increase in HS-ω3 index were observed in all subjects [-4.1 mg/dL, (SD:±51.7), P=.02 and 2.6%, (SD:±1.2), P<.001 respectively]. Mean fasting insulin and glycated hemoglobin (HbA1c%) were significantly decreased in all subjects [-0.547mlU/L, (SD:±10.29), P=.034 and-0.07%, (SD:±0.3), P<.001 respectively], whereas there was no change in body composition, fasting glucose, adiponectin and inflammatory markers. Subjects carrying the minor alleles of PPARα L162V and PPARγ2 P12A had higher responses in reduction of TG and fasting insulin respectively. Interestingly, doses below 2.7 g/day (1.8 g/day) were sufficient to induce a significant reduction in fasting insulin and HbA1c% from baseline (P=.019 and P<.001). The observed responses in triglycerides and fasting insulin in the Mexican population give further evidence of the importance of FO supplementation in young people as an early step towards the prevention of cardiometabolic disease.


Subject(s)
Biomarkers/blood , Fish Oils/pharmacology , Lipids/blood , PPAR alpha/genetics , PPAR gamma/genetics , Adult , Body Composition/drug effects , Dietary Sucrose , Dietary Supplements , Fatty Acids, Omega-3/administration & dosage , Female , Gene Frequency , Humans , Male , Mexico , Treatment Outcome , Triglycerides/blood
13.
Mech Ageing Dev ; 165(Pt B): 171-179, 2017 07.
Article in English | MEDLINE | ID: mdl-28017698

ABSTRACT

Systems biology approaches have been increasingly employed in clinical studies to enhance our understanding of the role of genetics, environmental factors and their interactions on nutritional, health and disease status. Amongst the new omics technologies, metabonomics has emerged as a robust platform to capture metabolic and nutritional requirements by enabling, in a minimally invasive fashion, the monitoring of a wide range of biochemical compounds. Their variations reflect comprehensively the various molecular regulatory processes, which are tightly controlled and under the influence of genetics, diet, gut microbiota and other environmental factors. They are providing key insights into complex metabolic phenomena as well as into differences and specificities at individual and population level. The aim of this review is to evaluate promising metabolic insights towards understanding metabolism of a long and healthy life from pre-clinical and clinical metabonomics studies. We will also discuss analytical approaches to enable data integration, with an emphasis on the longitudinal component. Herein, we will illustrate current examples, challenges and perspectives in the applications of metabonomics monitoring and modelling approaches in the context of healthy ageing research.


Subject(s)
Aging/metabolism , Metabolome/physiology , Metabolomics , Animals , Humans
14.
Anal Bioanal Chem ; 409(1): 295-305, 2017 Jan.
Article in English | MEDLINE | ID: mdl-27757515

ABSTRACT

The methionine cycle is a key pathway contributing to the regulation of human health, with well-established involvement in cardiovascular diseases and cognitive function. Changes in one-carbon cycle metabolites have also been associated with mild cognitive decline, vascular dementia, and Alzheimer's disease. Today, there is no single analytical method to monitor both metabolites and co-factors of the methionine cycle. To address this limitation, we here report for the first time a new method for the simultaneous quantitation of 17 metabolites in the methionine cycle, which are homocysteic acid, taurine, serine, cysteine, glycine, homocysteine, riboflavin, methionine, pyridoxine, cystathionine, pyridoxamine, S-adenosylhomocysteine, S-adenosylmethionine, betaine, choline, dimethylglycine, and 5-methyltetrahydrofolic acid. This multianalyte method, developed using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), provides a highly accurate and precise quantitation of these 17 metabolites for both plasma and cerebrospinal fluid metabolite monitoring. The method requires a simple sample preparation, which, combined with a short chromatographic run time, ensures a high sample throughput. This analytical strategy will thus provide a novel metabolomics approach to be employed in large-scale observational and intervention studies. We expect such a robust method to be particularly relevant for broad and deep molecular phenotyping of individuals in relation to their nutritional requirements, health monitoring, and disease risk management.


Subject(s)
Chromatography, High Pressure Liquid/methods , Homocysteine/blood , Homocysteine/cerebrospinal fluid , Metabolomics/methods , Methionine/blood , Methionine/cerebrospinal fluid , Tandem Mass Spectrometry/methods , High-Throughput Screening Assays/methods , Homocysteine/metabolism , Humans , Indicator Dilution Techniques , Limit of Detection , Metabolic Networks and Pathways , Methionine/metabolism , Middle Aged
15.
Bioanalysis ; 8(18): 1937-49, 2016 Sep.
Article in English | MEDLINE | ID: mdl-27558871

ABSTRACT

AIM: There is increasing interest in the profiling and quantitation of methionine pathway metabolites for health management research. Currently, several analytical approaches are required to cover metabolites and co-factors. RESULTS: We report the development and the validation of a method for the simultaneous detection and quantitation of 13 metabolites in red blood cells. The method, validated in a cohort of healthy human volunteers, shows a high level of accuracy and reproducibility. CONCLUSION: This high-throughput protocol provides a robust coverage of central metabolites and co-factors in one single analysis and in a high-throughput fashion. In large-scale clinical settings, the use of such an approach will significantly advance the field of nutritional research in health and disease.


Subject(s)
Chromatography, High Pressure Liquid/methods , Erythrocytes/metabolism , Homocysteine/metabolism , Methionine/metabolism , Nutritional Status , Tandem Mass Spectrometry/methods , Adolescent , Child , Cohort Studies , Erythrocytes/chemistry , Female , High-Throughput Screening Assays/methods , Homocysteine/analysis , Humans , Limit of Detection , Male , Metabolic Networks and Pathways , Methionine/analysis , Reproducibility of Results
16.
Anal Chem ; 88(15): 7617-26, 2016 08 02.
Article in English | MEDLINE | ID: mdl-27396289

ABSTRACT

Longitudinal studies aim typically at following populations of subjects over time and are important to understand the global evolution of biological processes. When it comes to longitudinal omics data, it will often depend on the overall objective of the study, and constraints imposed by the data, to define the appropriate modeling tools. Here, we report the use of multilevel simultaneous component analysis (MSCA), orthogonal projection on latent structures (OPLS), and regularized canonical correlation analysis (rCCA) to study associations between specific longitudinal urine metabonomics data and microbiome data in a diet-induced obesity model using C57BL/6 mice. (1)H NMR urine metabolic profiling was performed on samples collected weekly over a period of 13 weeks, and stool microbial composition was assessed using 16S rRNA gene sequencing at three specific time periods (baseline, first week response, end of study). MSCA and OPLS allowed us to explore longitudinal urine metabonomics data in relation to the dietary groups, as well as dietary effects on body weight. In addition, we report a data integration strategy based on regularized CCA and correlation analyses of urine metabonomics data and 16S rRNA gene sequencing data to investigate the functional relationships between metabolites and gut microbial composition. Thanks to this workflow enabling the breakdown of this data set complexity, the most relevant patterns could be extracted to further explore physiological processes at an anthropometric, cellular, and molecular level.


Subject(s)
Diet, High-Fat , Metabolomics , Microbiota , Animals , Bacteria/genetics , Bacteria/isolation & purification , Body Weight , Feces/microbiology , Least-Squares Analysis , Longitudinal Studies , Magnetic Resonance Spectroscopy , Male , Metabolome , Mice , Mice, Inbred C57BL , Principal Component Analysis , RNA, Ribosomal, 16S/chemistry , RNA, Ribosomal, 16S/genetics , RNA, Ribosomal, 16S/metabolism , Sequence Analysis, DNA , Urinalysis
17.
Obesity (Silver Spring) ; 23(1): 130-7, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25400283

ABSTRACT

OBJECTIVES: A lipidomic approach was employed in a clinically well-defined cohort of healthy obese women to explore blood lipidome phenotype ascribed to body fat deposition, with emphasis on epicardial adipose tissue (EAT). METHODS: The present investigation delivered a lipidomics signature of epicardial adiposity under healthy clinical conditions using a cohort of 40 obese females (age: 25-45 years, BMI: 28-40 kg/m(2) ) not showing any metabolic disease traits. Lipidomics analysis of blood plasma was employed in combination with in vivo quantitation of mediastinal fat depots by computerized tomography. RESULTS: All cardiac fat depots correlated to indicators of hepatic dysfunctions (ALAT and ASAT), which describe physiological connections between hepatic and cardiac steatosis. Plasma lipidomics encompassed overall levels of lipid classes, fatty acid profiles, and individual lipid species. EAT and visceral fat associated with diacylglycerols (DAG), triglycerides, and distinct phospholipid and sphingolipid species. A pattern of DAG and phosphoglycerols was specific to EAT. CONCLUSIONS: Human blood plasma lipidomics appears to be a promising clinical and potentially diagnostic readout for patient stratification and monitoring. Association of blood lipidomics signature to regio-specific mediastinal and visceral adiposity under healthy clinical conditions may help provide more biological insights into obese patient stratification for cardiovascular disease risks.


Subject(s)
Adipose Tissue/metabolism , Adiposity , Lipids/blood , Obesity/blood , Pericardium/metabolism , Adipose Tissue/diagnostic imaging , Adult , Cohort Studies , Diglycerides/blood , Fatty Acids/blood , Female , Health , Humans , Metabolomics , Middle Aged , Obesity/diagnostic imaging , Obesity/metabolism , Pericardium/diagnostic imaging , Phospholipids/blood , Sphingolipids/blood , Tomography, X-Ray Computed , Triglycerides/blood , Young Adult
18.
Inflamm Bowel Dis ; 20(11): 2104-14, 2014 Nov.
Article in English | MEDLINE | ID: mdl-25029616

ABSTRACT

Although the prevalence of main idiopathic forms of inflammatory bowel disease (IBD) has risen considerably over the last decades, their clinical features do not allow accurate prediction of prognosis, likelihood of disease progression, or response to specific therapy. Through a better understanding of the molecular pathways involved in IBD and the promise of more targeted therapies, the personalized approach to the management of IBD shows potential. To achieve this, there remains a significant need to better understand the disease process at cellular and molecular levels for any given individual with IBD. The complexity of biological functional networks behind the etiology of IBD highlights the need for their comprehensive analysis. In this, omics technologies can generate a systemic view of IBD pathogenesis on which to base novel, multiple pathway-integrated therapies. Omics sciences have just started to contribute here by generating gene, protein expression, metabolite data at global level and large scale, and more recently by offering new opportunities to explore gut functional ecology. In particular, there is much expectation regarding the putative role of the gut microbiome in IBD. No doubt it will provide additional insights and lead to the development of alternative, hopefully better, diagnostic, prognostic, and monitoring tools in the management of IBD. This review discusses perspectives of relevance to clinical translation with emphasis on gut microbial metabolic activities.


Subject(s)
Gastrointestinal Tract/metabolism , Gastrointestinal Tract/microbiology , Inflammatory Bowel Diseases/metabolism , Inflammatory Bowel Diseases/microbiology , Systems Biology/methods , Animals , Gastrointestinal Tract/pathology , Humans , Inflammatory Bowel Diseases/pathology , Prognosis
19.
PLoS Genet ; 10(2): e1004132, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24586186

ABSTRACT

Metabolic traits are molecular phenotypes that can drive clinical phenotypes and may predict disease progression. Here, we report results from a metabolome- and genome-wide association study on (1)H-NMR urine metabolic profiles. The study was conducted within an untargeted approach, employing a novel method for compound identification. From our discovery cohort of 835 Caucasian individuals who participated in the CoLaus study, we identified 139 suggestively significant (P<5×10(-8)) and independent associations between single nucleotide polymorphisms (SNP) and metabolome features. Fifty-six of these associations replicated in the TasteSensomics cohort, comprising 601 individuals from São Paulo of vastly diverse ethnic background. They correspond to eleven gene-metabolite associations, six of which had been previously identified in the urine metabolome and three in the serum metabolome. Our key novel findings are the associations of two SNPs with NMR spectral signatures pointing to fucose (rs492602, P = 6.9×10(-44)) and lysine (rs8101881, P = 1.2×10(-33)), respectively. Fine-mapping of the first locus pinpointed the FUT2 gene, which encodes a fucosyltransferase enzyme and has previously been associated with Crohn's disease. This implicates fucose as a potential prognostic disease marker, for which there is already published evidence from a mouse model. The second SNP lies within the SLC7A9 gene, rare mutations of which have been linked to severe kidney damage. The replication of previous associations and our new discoveries demonstrate the potential of untargeted metabolomics GWAS to robustly identify molecular disease markers.


Subject(s)
Metabolome/genetics , Metabolomics , Polymorphism, Single Nucleotide/genetics , Urine , Amino Acid Transport Systems, Basic/genetics , Animals , Crohn Disease/genetics , Crohn Disease/metabolism , Fucosyltransferases/genetics , Fucosyltransferases/metabolism , Genome-Wide Association Study , Humans , Kidney Diseases/genetics , Kidney Diseases/metabolism , Magnetic Resonance Spectroscopy , Male , Mice , Galactoside 2-alpha-L-fucosyltransferase
20.
Aging (Albany NY) ; 6(1): 9-25, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24457528

ABSTRACT

As centenarians well represent the model of healthy aging, there are many important implications in revealing the underlying molecular mechanisms behind such successful aging. By combining NMR metabonomics and shot-gun lipidomics in serum we analyzed metabolome and lipidome composition of a group of centenarians with respect to elderly individuals. Specifically, NMR metabonomics profiling of serum revealed that centenarians are characterized by a metabolic phenotype distinct from that of elderly subjects, in particular regarding amino acids and lipid species. Shot- gun lipidomics approach displays unique changes in lipids biosynthesis in centenarians, with 41 differently abundant lipid species with respect to elderly subjects. These findings reveal phospho/sphingolipids as putative markers and biological modulators of healthy aging, in humans. Considering the particular actions of these metabolites, these data are suggestive of a better counteractive antioxidant capacity and a well-developed membrane lipid remodelling process in the healthy aging phenotype.


Subject(s)
Aging/blood , Phospholipids/blood , Sphingolipids/blood , Age Factors , Aged , Aged, 80 and over , Amino Acids/blood , Biomarkers/blood , Female , Healthy Volunteers , Humans , Longevity , Magnetic Resonance Spectroscopy , Male , Metabolomics/methods , Middle Aged
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