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Kaput J, Monteiro JP. Human Nutrition Research in the Data Era: Results of 11 Reports on the Effects of a Multiple-Micronutrient-Intervention Study. Nutrients 2024; 16:188. [PMID: 38257081 PMCID: PMC10819666 DOI: 10.3390/nu16020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Large datasets have been used in molecular and genetic research for decades, but only a few studies have included nutrition and lifestyle factors. Our team conducted an n-of-1 intervention with 12 vitamins and five minerals in 9- to 13-year-old Brazilian children and teens with poor healthy-eating indices. A unique feature of the experimental design was the inclusion of a replication arm. Twenty-six types of data were acquired including clinical measures, whole-genome mapping, whole-exome sequencing, and proteomic and a variety of metabolomic measurements over two years. A goal of this study was to use these diverse data sets to discover previously undetected physiological effects associated with a poor diet that include a more complete micronutrient composition. We summarize the key findings of 11 reports from this study that (i) found that LDL and total cholesterol and fasting glucose decreased in the population after the intervention but with inter-individual variation; (ii) associated a polygenic risk score that predicted baseline vitamin B12 levels; (iii) identified metabotypes linking diet intake, genetic makeup, and metabolic physiology; (iv) found multiple biomarkers for nutrient and food groups; and (v) discovered metabolites and proteins that are associated with DNA damage. This summary also highlights the limitations and lessons in analyzing diverse omic data.
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Affiliation(s)
| | - Jacqueline Pontes Monteiro
- Faculty of Medicine of Ribeirão Preto, Department of Pediatrics, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil;
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Kussmann M, Abe Cunha DH, Berciano S. Bioactive compounds for human and planetary health. Front Nutr 2023; 10:1193848. [PMID: 37545571 PMCID: PMC10400358 DOI: 10.3389/fnut.2023.1193848] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/15/2023] [Indexed: 08/08/2023] Open
Abstract
Bioactive compounds found in edible plants and foods are vital for human and planetary health, yet their significance remains underappreciated. These natural bioactives, as part of whole diets, ingredients, or supplements, can modulate multiple aspects of human health and wellness. Recent advancements in omic sciences and computational biology, combined with the development of Precision Nutrition, have contributed to the convergence of nutrition and medicine, as well as more efficient and affordable healthcare solutions that harness the power of food for prevention and therapy. Innovation in this field is crucial to feed a growing global population sustainably and healthily. This requires significant changes in our food system, spanning agriculture, production, distribution and consumption. As we are facing pressing planetary health challenges, investing in bioactive-based solutions is an opportunity to protect biodiversity and the health of our soils, waters, and the atmosphere, while also creating value for consumers, patients, communities, and stakeholders. Such research and innovation targets include alternative proteins, such as cellular agriculture and plant-derived protein; natural extracts that improve shelf-life as natural preservatives; upcycling of agricultural by-products to reduce food waste; and the development of natural alternatives to synthetic fertilizers and pesticides. Translational research and innovation in the field of natural bioactives are currently being developed at two levels, using a systems-oriented approach. First, at the biological level, the interplay between these compounds and the human host and microbiome is being elucidated through omics research, big data and artificial intelligence, to accelerate both discovery and validation. Second, at the ecosystem level, efforts are focused on producing diverse nutrient-rich, flavorful, and resilient, yet high-yield agricultural crops, and educating consumers to make informed choices that benefit both their health and the planet. Adopting a system-oriented perspective helps: unravel the intricate and dynamic relationships between bioactives, nutrition, and sustainability outcomes, harnessing the power of nature to promote human health and wellbeing; foster sustainable agriculture and protect the ecosystem. Interdisciplinary collaboration in this field is needed for a new era of research and development of practical food-based solutions for some of the most pressing challenges humanity and our planet are facing today.
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Affiliation(s)
- Martin Kussmann
- Kompetenzzentrum für Ernährung (KErn), Freising, Germany
- Kussmann Biotech GmbH, Nordkirchen, Germany
| | - David Henrique Abe Cunha
- Ideatomik Creative Industries, Botucatu, Brazil
- Institute of Biosciences, São Paulo State University, Rio Claro, Brazil
| | - Silvia Berciano
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States
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Day K, Dordevic AL, Truby H, Southey MC, Coort S, Murgia C. Transcriptomic changes in peripheral blood mononuclear cells with weight loss: systematic literature review and primary data synthesis. GENES AND NUTRITION 2021; 16:12. [PMID: 34281497 PMCID: PMC8287703 DOI: 10.1186/s12263-021-00692-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 07/08/2021] [Indexed: 12/18/2022]
Abstract
Background and objectives Peripheral blood mononuclear cells (PBMCs) have shown promise as a tissue sensitive to subtle and possibly systemic transcriptomic changes, and as such may be useful in identifying responses to weight loss interventions. The primary aim was to comprehensively evaluate the transcriptomic changes that may occur during weight loss and to determine if there is a consistent response across intervention types in human populations of all ages. Methods Included studies were randomised control trials or cohort studies that administered an intervention primarily designed to decrease weight in any overweight or obese human population. A systematic search of the literature was conducted to obtain studies and gene expression databases were interrogated to locate corresponding transcriptomic datasets. Datasets were normalised using the ArrayAnalysis online tool and differential gene expression was determined using the limma package in R. Over-represented pathways were explored using the PathVisio software. Heatmaps and hierarchical clustering were utilised to visualise gene expression. Results Seven papers met the inclusion criteria, five of which had raw gene expression data available. Of these, three could be grouped into high responders (HR, ≥ 5% body weight loss) and low responders (LR). No genes were consistently differentially expressed between high and low responders across studies. Adolescents had the largest transcriptomic response to weight loss followed by adults who underwent bariatric surgery. Seven pathways were altered in two out of four studies following the intervention and the pathway ‘cytoplasmic ribosomal proteins’ (WikiPathways: WP477) was altered between HR and LR at baseline in the two datasets with both groups. Pathways related to ‘toll-like receptor signalling’ were altered in HR response to the weight loss intervention in two out of three datasets. Conclusions Transcriptomic changes in PBMCs do occur in response to weight change. Transparent and standardised data reporting is needed to realise the potential of transcriptomics for investigating phenotypic features. Registration number PROSPERO: CRD42019106582 Supplementary Information The online version contains supplementary material available at 10.1186/s12263-021-00692-6.
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Affiliation(s)
- Kaitlin Day
- Department of Nutrition, Dietetics and Food, Monash University, Level 1, 264 Ferntree Gully Road, Notting Hill, Victoria, 3168, Australia.
| | - Aimee L Dordevic
- Department of Nutrition, Dietetics and Food, Monash University, Level 1, 264 Ferntree Gully Road, Notting Hill, Victoria, 3168, Australia
| | - Helen Truby
- School of Human Movement and Nutrition Sciences, University of Queensland, Brisbane, Australia
| | - Melissa C Southey
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Susan Coort
- Department of Bioinformatics-BiGCaT, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Chiara Murgia
- School of Agriculture and Food, The University of Melbourne, Melbourne, Australia
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Fuzo CA, da Veiga Ued F, Moco S, Cominetti O, Métairon S, Pruvost S, Charpagne A, Carayol J, Torrieri R, Silva WA, Descombes P, Kaput J, Monteiro JP. Contribution of genetic ancestry and polygenic risk score in meeting vitamin B12 needs in healthy Brazilian children and adolescents. Sci Rep 2021; 11:11992. [PMID: 34099811 PMCID: PMC8184816 DOI: 10.1038/s41598-021-91530-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/25/2021] [Indexed: 02/08/2023] Open
Abstract
Polymorphisms in genes related to the metabolism of vitamin B12 haven’t been examined in a Brazilian population.
To (a) determine the correlation between the local genetic ancestry components and vitamin B12 levels using ninety B12-related genes; (b) determine associations between these genes and their SNPs with vitamin B12 levels; (c) determine a polygenic risk score (PRS) using significant variants. This cross-sectional study included 168 children and adolescents, aged 9–13 years old. Total cobalamin was measured in plasma. Genotyping arrays and whole exome data were combined to yield ~ 7000 SNPs in 90 genes related to vitamin B12. The Efficient Local Ancestry Inference was used to estimate local ancestry for African (AFR), Native American, and European (EUR). The association between the genotypes and vitamin B12 levels were determined with generalized estimating equation.
Vitamin B12 levels were driven by positive (EUR) and negative (AFR, AMR) correlations with genetic ancestry. A set of 36 variants were used to create a PRS that explained 42% of vitamin level variation.
Vitamin B12 levels are influenced by genetic ancestry and a PRS explained almost 50% of the variation in plasma cobalamin in Brazilian children and adolescents.
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Affiliation(s)
- Carlos Alessandro Fuzo
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutics Sciences, University of São Paulo, Ribeirão Preto, Brazil
| | - Fábio da Veiga Ued
- Department of Pediatrics and Department of Health Sciences, Ribeirão Preto Medical School, Nutrition and Metabolism Section, University of São Paulo, Avenida Bandeirantes, 3900, Bairro Monte Alegre, Ribeirão Preto, SP, 14040-900, Brazil
| | - Sofia Moco
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteite Amsterdam, Amsterdam, The Netherlands
| | - Ornella Cominetti
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Sylviane Métairon
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Solenn Pruvost
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Aline Charpagne
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland.,Sophia Genetics, Campus Biotech, 1202, Geneva, Switzerland
| | - Jerome Carayol
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Raul Torrieri
- Center for Medical Genomics, Ribeirão Preto Medical School Hospital, University of São Paulo, Ribeirão Preto, Brazil
| | - Wilson Araujo Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Patrick Descombes
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland
| | - Jim Kaput
- Nestlé Research, Société Des Produits Nestlé SA, EPFL Innovation Park, H, 1015, Lausanne, Switzerland.,, Vydiant, Folsom, CA, USA
| | - Jacqueline Pontes Monteiro
- Department of Pediatrics and Department of Health Sciences, Ribeirão Preto Medical School, Nutrition and Metabolism Section, University of São Paulo, Avenida Bandeirantes, 3900, Bairro Monte Alegre, Ribeirão Preto, SP, 14040-900, Brazil.
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Costanzo S, Virgili F, Panico S. Will guidelines on alcohol consumption be personalized by a genetic approach? GENES & NUTRITION 2021; 16:2. [PMID: 33494697 PMCID: PMC7830050 DOI: 10.1186/s12263-021-00682-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022]
Affiliation(s)
- Simona Costanzo
- Department of Epidemiology and Prevention, IRCCS Neuromed, Pozzilli, IS, Italy.
| | - Fabio Virgili
- Council for Agricultural Research and Economics, Research Centre for Food and Nutrition, Rome, Italy
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, Federico II University, Naples, Italy.
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Horne JR. Strengthening the Reporting of Nutritional Genomics Research to Inform Knowledge Translation in Personalized Nutrition. Lifestyle Genom 2021; 14:43-48. [PMID: 33477140 DOI: 10.1159/000512544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 10/23/2020] [Indexed: 11/19/2022] Open
Abstract
The ultimate goal of researching nutrigenetic interactions is to be able to provide individuals with genetically-tailored nutrition advice (when evidence is sufficient) in an effort to optimize health outcomes. Accordingly, original research often discusses the potential for the results to inform genetically-tailored nutrition advice. Despite this, many studies do not report their methods, results, and discussion in a manner that is conducive to knowledge translation. With several consumer nutritional genomics companies now offering genetic testing for personalized nutrition, proper reporting of nutritional genomics research for knowledge translation is of vital importance. Common reporting errors relate to SNP and genotype reporting, results lacking detail, consideration of linkage disequilibrium, mechanisms of action/functional SNPs, details of dietary intake, and sample reporting. Because of this, knowledge translation professionals may be unable or challenged in their attempt to use the findings from such research to inform clinical practice in nutritional genomics and personalized nutrition. The present article provides an overview of the issues at hand. It further pre-sents a checklist as well as table and figure templates for researchers to use when reporting the results of original research in nutritional genomics to inform knowledge translation.
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Affiliation(s)
- Justine R Horne
- Centre nutrition, santé et société (NUTRISS) - Institut sur la nutrition et les aliments fonctionnels (INAF), Université Laval, Quebec City, Québec, Canada,
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Endorsing the STrengthening the Reporting of Observational Studies in Epidemiology-nutritional epidemiology (STROBE-nut) statement at Genes & Nutrition. GENES & NUTRITION 2019; 14:30. [PMID: 31832107 PMCID: PMC6859619 DOI: 10.1186/s12263-019-0655-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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de Roos B, Aura AM, Bronze M, Cassidy A, Conesa MTG, Gibney ER, Greyling A, Kaput J, Kerem Z, Knežević N, Kroon P, Landberg R, Manach C, Milenkovic D, Rodriguez-Mateos A, Tomás-Barberán FA, van de Wiele T, Morand C. Targeting the delivery of dietary plant bioactives to those who would benefit most: from science to practical applications. Eur J Nutr 2019; 58:65-73. [PMID: 31637468 PMCID: PMC6851046 DOI: 10.1007/s00394-019-02075-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/02/2019] [Indexed: 03/19/2023]
Abstract
Background A healthy diet and optimal lifestyle choices are amongst the most important actions for the prevention of cardiometabolic diseases. Despite this, it appears difficult to convince consumers to select more nutritious foods. Furthermore, the development and production of healthier foods do not always lead to economic profits for the agro-food sector. Most dietary recommendations for the general population represent a “one-size-fits-all approach” which does not necessarily ensure that everyone has adequate exposure to health-promoting constituents of foods. Indeed, we now know that individuals show a high variability in responses when exposed to specific nutrients, foods, or diets. Purpose This review aims to highlight our current understanding of inter-individual variability in response to dietary bioactives, based on the integration of findings of the COST Action POSITIVe. We also evaluate opportunities for translation of scientific knowledge on inter-individual variability in response to dietary bioactives, once it becomes available, into practical applications for stakeholders, such as the agro-food industry. The potential impact from such applications will form an important impetus for the food industry to develop and market new high quality and healthy foods for specific groups of consumers in the future. This may contribute to a decrease in the burden of diet-related chronic diseases. Individual differences in ADME (Absorption, Digestion, Metabolism and Excretion) is believed to underpin much of the inter-individual variation in responses. Recent developments in the area of food metabolome databases and fast improvements in innovative metabotyping technologies hold great promise for improved profiling of dietary intake, exposure to individual ingredients, foods and dietary patterns, as well as our ability to identify individual responsiveness. The food industry needs well-defined population clusters or targets in order to be able to design “personalized products”. There are indeed excellent industrial opportunities for foods that modulate gut microbiota, and thereby enable the delivery of food bioactive metabolites. It is currently not clear whether knowledge on individual nutrient needs, based on genetic or metagenomic data, would affect long-term dietary and health behaviours. Data to support the development of dietary recommendations may need to be generated by new n-of-1-based study designs in the future.
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Affiliation(s)
- Baukje de Roos
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
| | - Anna-Marja Aura
- VTT Technical Research Centre of Finland, PO Box 1000, Tietotie 2, Espoo, Finland
| | - Maria Bronze
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, Portugal
| | - Aedin Cassidy
- Department of Nutrition and Preventive Medicine, Norwich Medical School, University of East Anglia, Norwich, UK
| | - María-Teresa Garcia Conesa
- Food and Health Laboratory. Research Group on Quality, Safety, and Bioactivity of Plant Foods, CEBAS-CSIC, Campus de Espinardo, Murcia, Spain
| | - Eileen R Gibney
- UCD Institute of Food and Health, School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Arno Greyling
- Unilever Research and Development Vlaardingen, Vlaardingen, The Netherlands
| | | | - Zohar Kerem
- R.H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Paul Kroon
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Rikard Landberg
- Division of Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Claudine Manach
- INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Dragan Milenkovic
- INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ana Rodriguez-Mateos
- Department of Nutritional Sciences, Faculty of Life Sciences and Medicine, School of Life Course Sciences, King's College London, London, UK
| | - Francisco A Tomás-Barberán
- Food and Health Laboratory. Research Group on Quality, Safety, and Bioactivity of Plant Foods, CEBAS-CSIC, Campus de Espinardo, Murcia, Spain
| | - Tom van de Wiele
- Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Christine Morand
- INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, Université Clermont Auvergne, Clermont-Ferrand, France
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