Special Issue "Genomics and Personalized Nutrition"

A special issue of Nutrients (ISSN 2072-6643). This special issue belongs to the section "Nutrigenetics and Nutrigenomics".

Deadline for manuscript submissions: closed (15 September 2020).

Special Issue Editors

Dr. Iwona Rudkowska
E-Mail Website
Guest Editor
Endocrinology and Nephrology Unit, CHU de Québec, Université Laval Research Center, Laurier Boulevard, QC, Canada;
Department of Kinesiology, Faculty of Medicine, Université Laval, Quebec, QC, Canada
Interests: nutrigenomics; nutrigenetics; personalized nutrition; functional genomics; gene–diet interactions; OMICs
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. M. Luisa Bonet
E-Mail Website
Guest Editor
Nutrigenomic and Obesity Research Group, Laboratory of Molecular Biology, Nutrition and Biotechnology (LBNB), University of the Balearic Islands, Palma de Mallorca, Spain
Interests: Obesity; molecular nutrition; nutrigenomics; vitamin A; food bioactives
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Personalized nutrition aims to prevent the onset and development of chronic diseases, such as obesity, cardiovascular diseases, type 2 diabetes, and dyslipidemia, by targeting dietary recommendations to an individual’s characteristics. Research findings demonstrate clearly that some individuals may benefit from adhering to different dietary guidelines than others. These days, the incorporation of genomics technologies can be used to better personalize the diet based on biological responses to foods/nutrients in addition to the better understanding of metabolic pathways relevant to disease risk.

The purpose of this Special Issue is to expand and add to the research which uses genomics technologies (genetics, epigenetics, transcriptomics, metabolomics, and microbiomics) in the development of personalized nutrition therapies. Submissions may include studies focused on the investigation of the effects of specific diets, dietary patterns, foods, nutrients, or bioactive compounds on changes in genomics parameters that could modify the biological responses and/or the risk of chronic diseases. This issue welcomes the submission of manuscripts describing related original research or reviews of the scientific literature in humans (interventional, observational, cohort studies) or animal models.

Dr. Iwona Rudkowska
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Nutrients is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Nutrigenomics
  • Nutrigenetics
  • Personalized nutrition
  • Functional genomics
  • Gene–diet interactions
  • OMICs

Published Papers (10 papers)

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Editorial

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Editorial
Genomics and Personalized Nutrition
Nutrients 2021, 13(4), 1128; https://0-doi-org.brum.beds.ac.uk/10.3390/nu13041128 - 30 Mar 2021
Viewed by 844
Abstract
Genomics technologies can be used to study the relationship between the human genome, nutrition, and health [...] Full article
(This article belongs to the Special Issue Genomics and Personalized Nutrition)

Research

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Article
Polygenetic-Risk Scores Related to Crystallin Metabolism Are Associated with Age-Related Cataract Formation and Interact with Hyperglycemia, Hypertension, Western-Style Diet, and Na Intake
Nutrients 2020, 12(11), 3534; https://0-doi-org.brum.beds.ac.uk/10.3390/nu12113534 - 17 Nov 2020
Cited by 1 | Viewed by 945
Abstract
Age-related cataract (ARC) development is associated with loss of crystalline lens transparency related to interactions between genetic and environmental factors. We hypothesized that polygenetic risk scores (PRS) of the selected genetic variants among the ARC-related genes might reveal significant genetic impacts on ARC [...] Read more.
Age-related cataract (ARC) development is associated with loss of crystalline lens transparency related to interactions between genetic and environmental factors. We hypothesized that polygenetic risk scores (PRS) of the selected genetic variants among the ARC-related genes might reveal significant genetic impacts on ARC risk, and the PRS might have gene–gene and gene–lifestyle interactions. We examined the hypothesis in 1972 and 39,095 subjects aged ≥50 years with and without ARC, respectively, in a large-scale hospital-based cohort study conducted from 2004 to 2013. Single nucleotide polymorphisms (SNPs) of the genes related to ARC risk were identified, and polygenetic risk scores (PRS) were generated based on the results of a generalized multifactor dimensionality reduction analysis. Lifestyle interactions with PRS were evaluated. The PRS derived from the best model included the following six SNPs related to crystallin metabolism: ULK4_rs1417380362, CRYAB_rs2070894, ACCN1_rs55785344, SSTR2_rs879419608, PTN_rs322348, and ICA1_rs200053781. The risk of ARC in the high-PRS group was 2.47-fold higher than in the low-PRS group after adjusting for confounders. Age, blood pressure, and glycemia interacted with PRS to influence the risk of ARC: the incidence of ARC was much higher in the elderly (≥65 years) and individuals with hypertension or hyperglycemia. The impact of PRS on ARC risk was greatest in middle-aged individuals with hypertension or hyperglycemia. Na, coffee, and a Western-style diet intake also interacted with PRS to influence ARC risk. ARC risk was higher in the high-PRS group than in the low-PRS group, and high Na intake, Western-style diet, and low coffee intake elevated its risk. In conclusion, ARC risk had a positive association with PRS related to crystallin metabolism. The genetic impact was greatest among those with high Na intake or hypertension. These results can be applied to precision nutrition interventions to prevent ARC. Full article
(This article belongs to the Special Issue Genomics and Personalized Nutrition)
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Article
Animal and Cellular Studies Demonstrate Some of the Beneficial Impacts of Herring Milt Hydrolysates on Obesity-Induced Glucose Intolerance and Inflammation
Nutrients 2020, 12(11), 3235; https://0-doi-org.brum.beds.ac.uk/10.3390/nu12113235 - 22 Oct 2020
Cited by 6 | Viewed by 1127
Abstract
The search for bioactive compounds from enzymatic hydrolysates has increased in the last few decades. Fish by-products have been shown to be rich in these valuable molecules; for instance, herring milt is a complex matrix composed of lipids, nucleotides, minerals, and proteins. However, [...] Read more.
The search for bioactive compounds from enzymatic hydrolysates has increased in the last few decades. Fish by-products have been shown to be rich in these valuable molecules; for instance, herring milt is a complex matrix composed of lipids, nucleotides, minerals, and proteins. However, limited information is available on the potential health benefits of this by-product. In this context, three industrial products containing herring milt hydrolysate (HMH) were tested in both animal and cellular models to measure their effects on obesity-related metabolic disorders. Male C57Bl/6J mice were fed either a control chow diet or a high-fat high-sucrose (HFHS) diet for 8 weeks and received either the vehicle (water) or one of the three HMH products (HMH1, HMH2, and HMH3) at a dose of 208.8 mg/kg (representing 1 g/day for a human) by daily oral gavage. The impact of HMH treatments on insulin and glucose tolerance, lipid homeostasis, liver gene expression, and the gut microbiota profile was studied. In parallel, the effects of HMH on glucose uptake and inflammation were studied in L6 myocytes and J774 macrophages, respectively. In vivo, daily treatment with HMH2 and HMH3 improved early time point glycemia during the oral glucose tolerance test (OGTT) induced by the HFHS diet, without changes in weight gain and insulin secretion. Interestingly, we also observed that HMH2 consumption partially prevented a lower abundance of Lactobacillus species in the gut microbiota of HFHS diet-fed animals. In addition to this, modulations of gene expression in the liver, such as the upregulation of sucrose nonfermenting AMPK-related kinase (SNARK), were reported for the first time in mice treated with HMH products. While HMH2 and HMH3 inhibited inducible nitric oxide synthase (iNOS) induction in J774 macrophages, glucose uptake was not modified in L6 muscle cells. These results indicate that milt herring hydrolysates reduce some metabolic and inflammatory alterations in cellular and animal models, suggesting a possible novel marine ingredient to help fight against obesity-related immunometabolic disorders. Full article
(This article belongs to the Special Issue Genomics and Personalized Nutrition)
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Article
A Genome-Wide Association Study Identifies the Association between the 12q24 Locus and Black Tea Consumption in Japanese Populations
Nutrients 2020, 12(10), 3182; https://0-doi-org.brum.beds.ac.uk/10.3390/nu12103182 - 18 Oct 2020
Cited by 2 | Viewed by 2598
Abstract
Several genome-wide association studies (GWASs) have reported the association between genetic variants and the habitual consumption of foods and drinks; however, no association data are available regarding the consumption of black tea. The present study aimed to identify genetic variants associated with black [...] Read more.
Several genome-wide association studies (GWASs) have reported the association between genetic variants and the habitual consumption of foods and drinks; however, no association data are available regarding the consumption of black tea. The present study aimed to identify genetic variants associated with black tea consumption in 12,258 Japanese participants. Data on black tea consumption were collected by a self-administered questionnaire, and genotype data were obtained from a single nucleotide polymorphism array. In the discovery GWAS, two loci met suggestive significance (p < 1.0 × 10−6). Three genetic variants (rs2074356, rs144504271, and rs12231737) at 12q24 locus were also significantly associated with black tea consumption in the replication stage (p < 0.05) and during the meta-analysis (p < 5.0 × 10−8). The association of rs2074356 with black tea consumption was slightly attenuated by the additional adjustment for alcohol drinking frequency. In conclusion, genetic variants at the 12q24 locus were associated with black tea consumption in Japanese populations, and the association is at least partly mediated by alcohol drinking frequency. Full article
(This article belongs to the Special Issue Genomics and Personalized Nutrition)
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Article
Current State of Evidence: Influence of Nutritional and Nutrigenetic Factors on Immunity in the COVID-19 Pandemic Framework
Nutrients 2020, 12(9), 2738; https://0-doi-org.brum.beds.ac.uk/10.3390/nu12092738 - 08 Sep 2020
Cited by 49 | Viewed by 18927
Abstract
The pandemic caused by the new coronavirus has caused shock waves in many countries, producing a global health crisis worldwide. Lack of knowledge of the biological mechanisms of viruses, plus the absence of effective treatments against the disease (COVID-19) and/or vaccines have pulled [...] Read more.
The pandemic caused by the new coronavirus has caused shock waves in many countries, producing a global health crisis worldwide. Lack of knowledge of the biological mechanisms of viruses, plus the absence of effective treatments against the disease (COVID-19) and/or vaccines have pulled factors that can compromise the proper functioning of the immune system to fight against infectious diseases into the spotlight. The optimal status of specific nutrients is considered crucial to keeping immune components within their normal activity, helping to avoid and overcome infections. Specifically, the European Food Safety Authority (EFSA) evaluated and deems six vitamins (D, A, C, Folate, B6, B12) and four minerals (zinc, iron, copper and selenium) to be essential for the normal functioning of the immune system, due to the scientific evidence collected so far. In this report, an update on the evidence of the contribution of nutritional factors as immune-enhancing aspects, factors that could reduce their bioavailability, and the role of the optimal status of these nutrients within the COVID-19 pandemic context was carried out. First, a non-systematic review of the current state of knowledge regarding the impact of an optimal nutritional status of these nutrients on the proper functioning of the immune system as well as their potential role in COVID-19 prevention/treatment was carried out by searching for available scientific evidence in PubMed and LitCovid databases. Second, a compilation from published sources and an analysis of nutritional data from 10 European countries was performed, and the relationship between country nutritional status and epidemiological COVID-19 data (available in the Worldometers database) was evaluated following an ecological study design. Furthermore, the potential effect of genetics was considered through the selection of genetic variants previously identified in Genome-Wide Association studies (GWAs) as influencing the nutritional status of these 10 considered nutrients. Therefore, access to genetic information in accessible databases (1000genomes, by Ensembl) of individuals from European populations enabled an approximation that countries might present a greater risk of suboptimal status of the nutrients studied. Results from the review approach show the importance of maintaining a correct nutritional status of these 10 nutrients analyzed for the health of the immune system, highlighting the importance of Vitamin D and iron in the context of COVID-19. Besides, the ecological study demonstrates that intake levels of relevant micronutrients—especially Vitamins D, C, B12, and iron—are inversely associated with higher COVID-19 incidence and/or mortality, particularly in populations genetically predisposed to show lower micronutrient status. In conclusion, nutrigenetic data provided by joint assessment of 10 essential nutrients for the functioning of the immune system and of the genetic factors that can limit their bioavailability can be a fundamental tool to help strengthen the immune system of individuals and prepare populations to fight against infectious diseases such as COVID-19. Full article
(This article belongs to the Special Issue Genomics and Personalized Nutrition)
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Article
Impaired CPT1A Gene Expression Response to Retinoic Acid Treatment in Human PBMC as Predictor of Metabolic Risk
Nutrients 2020, 12(8), 2269; https://0-doi-org.brum.beds.ac.uk/10.3390/nu12082269 - 29 Jul 2020
Cited by 2 | Viewed by 1200
Abstract
Ex vivo human peripheral blood mononuclear cell (PBMC) systems offer the possibility to test transcriptomic effects of food bioactive compounds with potential health effects. We investigated all-trans retinoic acid (ATRA) effect on mRNA expression of key lipid metabolism and inflammatory genes in PBMCs [...] Read more.
Ex vivo human peripheral blood mononuclear cell (PBMC) systems offer the possibility to test transcriptomic effects of food bioactive compounds with potential health effects. We investigated all-trans retinoic acid (ATRA) effect on mRNA expression of key lipid metabolism and inflammatory genes in PBMCs from normal-weight (NW) and overweight-obese (OW-OB) men with different metabolic syndrome-related features. PBMCs were incubated with 10 µM ATRA and mRNA levels of selected genes were analyzed using real-time RT-qPCR. Human ex vivo PBMCs responded to ATRA treatment, but the response for some genes was dependent on body mass index (BMI), with a lower response in PBMC from OW-OB than from NW donors. Moreover, gene expression response was affected by circulating high-density lipoprotein (HDL)-cholesterol levels. Particularly, the response to ATRA of CPT1A, previously reported as a sensitive metabolic risk predictive biomarker, was dependent on HDL levels and not on BMI, being impaired in those individuals with lower HDL levels, specifically in OW-OB. Thus, PBMCs’ insensitivity to ATRA, which can be considered as indicative of impaired metabolism, was observed in individuals with higher metabolic risk (OW-OB with low HDL levels). In conclusion, an ex vivo human PBMC system indicates that ATRA response could be influenced by metabolic syndrome features. Moreover, our study reinforces the role of CPT1A as a marker of metabolic risk and points to plasmatic HDL-cholesterol levels as a parameter to take into consideration when the effects of nutritional factors and/or dietary interventions on humans are under study. Further studies including women are required to detect potential gender differences in the observed effects. Full article
(This article belongs to the Special Issue Genomics and Personalized Nutrition)
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Review

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Review
Statistical and Machine-Learning Analyses in Nutritional Genomics Studies
Nutrients 2020, 12(10), 3140; https://0-doi-org.brum.beds.ac.uk/10.3390/nu12103140 - 14 Oct 2020
Cited by 3 | Viewed by 1672
Abstract
Nutritional compounds may have an influence on different OMICs levels, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and metagenomics. The integration of OMICs data is challenging but may provide new knowledge to explain the mechanisms involved in the metabolism of nutrients and diseases. Traditional [...] Read more.
Nutritional compounds may have an influence on different OMICs levels, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and metagenomics. The integration of OMICs data is challenging but may provide new knowledge to explain the mechanisms involved in the metabolism of nutrients and diseases. Traditional statistical analyses play an important role in description and data association; however, these statistical procedures are not sufficiently enough powered to interpret the large integrated multiple OMICs (multi-OMICS) datasets. Machine learning (ML) approaches can play a major role in the interpretation of multi-OMICS in nutrition research. Specifically, ML can be used for data mining, sample clustering, and classification to produce predictive models and algorithms for integration of multi-OMICs in response to dietary intake. The objective of this review was to investigate the strategies used for the analysis of multi-OMICs data in nutrition studies. Sixteen recent studies aimed to understand the association between dietary intake and multi-OMICs data are summarized. Multivariate analysis in multi-OMICs nutrition studies is used more commonly for analyses. Overall, as nutrition research incorporated multi-OMICs data, the use of novel approaches of analysis such as ML needs to complement the traditional statistical analyses to fully explain the impact of nutrition on health and disease. Full article
(This article belongs to the Special Issue Genomics and Personalized Nutrition)
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Review
Genomics in Personalized Nutrition: Can You “Eat for Your Genes”?
Nutrients 2020, 12(10), 3118; https://0-doi-org.brum.beds.ac.uk/10.3390/nu12103118 - 13 Oct 2020
Cited by 13 | Viewed by 4966
Abstract
Genome-wide single nucleotide polymorphism (SNP) data are now quickly and inexpensively acquired, raising the prospect of creating personalized dietary recommendations based on an individual’s genetic variability at multiple SNPs. However, relatively little is known about most specific gene–diet interactions, and many molecular and [...] Read more.
Genome-wide single nucleotide polymorphism (SNP) data are now quickly and inexpensively acquired, raising the prospect of creating personalized dietary recommendations based on an individual’s genetic variability at multiple SNPs. However, relatively little is known about most specific gene–diet interactions, and many molecular and clinical phenotypes of interest (e.g., body mass index [BMI]) involve multiple genes. In this review, we discuss direct to consumer genetic testing (DTC-GT) and the current potential for precision nutrition based on an individual’s genetic data. We review important issues such as dietary exposure and genetic architecture addressing the concepts of penetrance, pleiotropy, epistasis, polygenicity, and epigenetics. More specifically, we discuss how they complicate using genotypic data to predict phenotypes as well as response to dietary interventions. Then, several examples (including caffeine sensitivity, alcohol dependence, non-alcoholic fatty liver disease, obesity/appetite, cardiovascular, Alzheimer’s disease, folate metabolism, long-chain fatty acid biosynthesis, and vitamin D metabolism) are provided illustrating how genotypic information could be used to inform nutritional recommendations. We conclude by examining ethical considerations and practical applications for using genetic information to inform dietary choices and the future role genetics may play in adopting changes beyond population-wide healthy eating guidelines. Full article
(This article belongs to the Special Issue Genomics and Personalized Nutrition)
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Review
Genetic and Physiological Factors Affecting Human Milk Production and Composition
Nutrients 2020, 12(5), 1500; https://0-doi-org.brum.beds.ac.uk/10.3390/nu12051500 - 21 May 2020
Cited by 5 | Viewed by 2603
Abstract
Human milk is considered the optimal nutrition for infants as it provides additional attributes other than nutritional support for the infant and contributes to the mother’s health as well. Although breastfeeding is the most natural modality to feed infants, nowadays, many mothers complain [...] Read more.
Human milk is considered the optimal nutrition for infants as it provides additional attributes other than nutritional support for the infant and contributes to the mother’s health as well. Although breastfeeding is the most natural modality to feed infants, nowadays, many mothers complain about breastfeeding difficulties. In addition to environmental factors that may influence lactation outcomes including maternal nutrition status, partner’s support, stress, and latching ability of the infant, intrinsic factors such as maternal genetics may also affect the quantitative production and qualitative content of human milk. These genetic factors, which may largely affect the infant’s growth and development, as well as the mother’s breastfeeding experience, are the subject of the present review. We specifically describe genetic variations that were shown to affect quantitative human milk supply and/or its qualitative content. We further discuss possible implications and methods for diagnosis as well as treatment modalities. Although cases of nutrient-deficient human milk are considered rare, in some ethnic groups, genetic variations that affect human milk content are more abundant, and they should receive greater attention for diagnosis and treatment when necessary. From a future perspective, early genetic diagnosis should be directed to target and treat breastfeeding difficulties in real time. Full article
(This article belongs to the Special Issue Genomics and Personalized Nutrition)
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Review
Direct-to-Consumer Nutrigenetics Testing: An Overview
Nutrients 2020, 12(2), 566; https://0-doi-org.brum.beds.ac.uk/10.3390/nu12020566 - 21 Feb 2020
Cited by 8 | Viewed by 3481
Abstract
At present, specialized companies offering genetic testing services without the involvement of clinicians are growing; this development is a direct consequence of the significant decrease in genotyping and sequencing costs. Online companies offer predictions about the risk of developing complex diseases during one’s [...] Read more.
At present, specialized companies offering genetic testing services without the involvement of clinicians are growing; this development is a direct consequence of the significant decrease in genotyping and sequencing costs. Online companies offer predictions about the risk of developing complex diseases during one’s life course, and they offer suggestions for personal lifestyle. Several companies have been created that provide nutrigenetics services; these companies suggest dietary indications—a central issue in the prevention and etiopathogenesis of specific diseases—based on one’s personal genetic background. Dietary patterns are defined on the basis of a limited set of genetic markers. In this article, we analyze the online nutrigenetics services offered by 45 companies worldwide, to obtain an overall picture of the costs, the types of nutritional traits considered and the level of scientific precision of the services proposed. Our analysis clearly highlights the need for specific guidelines, in order to ensure a set of minimum quality standards for the nutrigenetics services offered to the customer. Full article
(This article belongs to the Special Issue Genomics and Personalized Nutrition)
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