Nutritional genomics: the next frontier in the postgenomic era

Effects of Mediterranean diets and nutrigenomics on cardiovascular health

The field of nutrigenomics studies the interaction between nutrition and genetics, and how certain dietary patterns can impact gene expression and overall health. The Mediterranean diet (MedDiet), characterized by a high intake of fruits, vegetables, whole grains, and healthy fats, has been linked to better cardiovascular health (CVH) outcomes. This review summarizes the current state of research on the effects of nutrigenomics and MedDiet on cardiovascular health. Results suggest that MedDiet, through its impact on gene expression, can positively influence CVH markers such as blood pressure, lipid profile, and inflammation. However, more research is needed to fully understand the complex interactions between genetics, nutrition, and CVH, and to determine the optimal dietary patterns for individualized care. The aim of this scientific review is to evaluate the current evidence on the effects of nutrigenomics and MedDiet on cardiovascular health. The review summarizes the available studies that have investigated the relationship between nutrition, genetics, and cardiovascular health, and explores the mechanisms by which certain dietary patterns can impact CVH outcomes. The review focuses on the effects of MedDiet, a dietary pattern that is rich in whole foods and healthy fats, and its potential to positively influence CVH through its impact on gene expression. The review highlights the limitations of current research and the need for further studies to fully understand the complex interplay between nutrition, genetics, and cardiovascular health.

Current insights into genome-based personalized nutrition technology: a patent review

Unlike general nutritional ranges that meet the nutritional needs essential for maintaining the life of an entire population, personalized nutrition is characterised by maintaining health through providing customized nutrition according to individuals' lifestyles or genetic characteristics. The development of technology and services for personalized nutrition is increasing, owing to the acquisition of knowledge about the differences in nutritional requirements according to the diversity of individuals and an increase in health interest. Regarding genetics, technology is being developed to distinguish the various characteristics of individuals and provide customized nutrition. Therefore, to understand the current state of personalized nutrition technology, understanding genomics is necessary to acquire information on nutrition research based on genomics. We reviewed patents related to personalized nutrition-targeting genomics and examined their mechanisms of action. Using the patent database, we searched 694 patents on nutritional genomics and extracted 561 highly relevant valid data points. Furthermore, an in-depth review was conducted by selecting core patents related to genome-based personalized nutrition technology. A marked increase was observed in personalized nutrition technologies using methods such as genetic scoring and disease-specific dietary recommendations.

Nutritional Genomics and Cancer Prevention

The scientific innovations have emphasized the importance of diet for one's health and wellbeing. The genetic revolution has enhanced our understanding about the effect of nutrients on genomic and transcriptomic profiles and gene-nutrition interactions (nutritional genomics). Furthermore, the contribution of micronutrient insufficiencies and macronutrient excess is evident in the development and progression of many diseases, especially cancer. It is speculated that nutrients have capacity to implicitly affect the physiological and pathophysiological processes via gene expression various regulatory processes. Moreover, the nutrients are known to affect the cellular networks involved in cancer progression and cancer inhibitory mechanisms targeting apoptosis or impaired angiogenesis. The interplay of regulatory processes in physiological systems and nutrients provides basis for the nutrigenomics. The functional genomics data further argue that cellular and molecular processes involved in the cancer progression are possibly programed genes during early development which may persist into adulthood and become detrimental. The incorporation of the functional interactions between nutrients and the genome has revolutionized the field of personalized medicine and provided the foundation for targeted cancer therapy through nutrients. There is growing evidence on the beneficial impacts of eating habits on lowering the risk of cancer, even if it can be difficult to pinpoint the precise role of nutrients. The nutrigenomic information may provide bases to develop disease prevention and treatment via nutrition, at the molecular level.

Unveiling the future of metabolic medicine: omics technologies driving personalized solutions for precision treatment of metabolic disorders

Metabolic disorders are increasingly prevalent worldwide, leading to high rates of morbidity and mortality. The variety of metabolic illnesses can be addressed through personalized medicine. The goal of personalized medicine is to give doctors the ability to anticipate the best course of treatment for patients with metabolic problems. By analyzing a patient's metabolomic, proteomic, genetic profile, and clinical data, physicians can identify relevant diagnostic, and predictive biomarkers and develop treatment plans and therapy for acute and chronic metabolic diseases. To achieve this goal, real-time modeling of clinical data and multiple omics is essential to pinpoint underlying biological mechanisms, risk factors, and possibly useful data to promote early diagnosis and prevention of complex diseases. Incorporating cutting-edge technologies like artificial intelligence and machine learning is crucial for consolidating diverse forms of data, examining multiple variables, establishing databases of clinical indicators to aid decision-making, and formulating ethical protocols to address concerns. This review article aims to explore the potential of personalized medicine utilizing omics approaches for the treatment of metabolic disorders. It focuses on the recent advancements in genomics, epigenomics, proteomics, metabolomics, and nutrigenomics, emphasizing their role in revolutionizing personalized medicine.

Dietary supplementation with olive oil co-products rich in polyphenols: a novel nutraceutical approach in monogastric animal nutrition

In recent years, the increased demand for agri-food products to feed livestock species has stimulated research to identify novel solutions for the valorization of natural waste, according to the modern concept of a circular economy. Numerous studies have shown the use of plant-derived and agro-industrial co-products that are sources of bioactive molecules for preparing animal feeds. Supplementation with co-products derived from the extraction of olive oil (i.e., olive pomace, olive mill wastewater, olive cake and olive leaf) in diet has been widely considered in recent decades, because these wastes are produced in high quantity and their re-use represents an innovative economic and environmental strategy. Olive oil co-products are characterized by various bioactive molecules such as polyphenols, carbohydrates, proteins, and lipids. Among them, polyphenols are the nutraceuticals most studied, showing to promote health effects in both humans and animals. Olive oil co-products and their phenolic extracts have shown many beneficial and promising effects when added to the diets of monogastric animals, by improving performance parameters and maintaining the oxidative status of meat and derived products. This review provides an update on the use of olive co-products in monogastric animal (swine, poultry and rabbit) diets and their effects on the productive performance, meat quality characteristics and gut health status.

Advances in Nutrigenomics and Applications in Public Health: A Recent Update

Nutrition research is achieving new paradigms through recent advances in the field of Nutrigenomics. The application of genomic principles for the identification of relationships between certain specific nutrients with genetic factors is termed “Nutrigenomics”. This knowledge is essential to understanding the risk factors behind diet-related chronic degenerative diseases, which further helps resolve the underlying mechanism of genetic predisposition. Advances in Sciences associated with the study of genes have assisted in developing a deep insight into genetic variants, and gene expression patterns to work out therapeutic responses toward chronic degenerative diseases associated with Public Health. To appraise recent advances in Nutrigenomics with its application in Public health several databases including Pub Med, Google Scholar, Medline etc were investigated in detail. A total of 72 relevant peer-reviewed journal articles were included in this review paper. Nutrigenomics has an important role in comprehending how homeostatic control is maintained and the way metabolic pathways are influenced by nutrient intake. The knowledge of Nutrigenomics helps in working out personalized nutrition strategies for both prevention and management of the diseased situation. The present review article aims to investigate and present a piece of in-depth information about the latest Advances in Nutrigenomics and its application in public health.

Emergence of nutrigenomics and dietary components as a complementary therapy in cancer prevention

Cancer is an illness characterized by abnormal cell development and the capability to infiltrate or spread to rest of the body. A tumor is the term for this abnormal growth that develops in solid tissues like an organ, muscle, or bone and can spread to other parts of the body through the blood and lymphatic systems. Nutrition is a critical and immortal environmental component in the development of all living organisms encoding the relationship between a person's nutrition and their genes. Nutrients have the ability to modify gene expression and persuade alterations in DNA and protein molecules which is researched scientifically in nutrigenomics. These interactions have a significant impact on the pharmacokinetic properties of bioactive dietary components as well as their site of action/molecular targets. Nutrigenomics encompasses nutrigenetics, epigenetics, and transcriptomics as well as other "omic" disciplines like proteomics and metabolomics to explain the vast disparities in cancer risk among people with roughly similar life style. Clinical trials and researches have evidenced that alternation of dietary habits is potentially one of the key approaches for reducing cancer risk in an individual. In this article, we will target how nutrigenomics and functional food work as preventive therapy in reducing the risk of cancer.

MicroRNA sensing and regulating microbiota-host crosstalk via diet motivation

Accumulating evidence has demonstrated that diet-derived gut microbiota participates in the regulation of host metabolism and becomes the foundation for precision-based nutritional interventions and the biomarker for potential individual dietary recommendations. However, the specific mechanism of the gut microbiota-host crosstalk remains unclear. Recent studies have identified that noncoding RNAs, as important elements in the regulation of the initiation and termination of gene expression, mediate microbiota-host communication. Besides, the cross-kingdom regulation of non-host derived microRNAs also influence microbiota-host crosstalk via diet motivation. Hence, understanding the relationship between gut microbiota, miRNAs, and host metabolism is indispensable to revealing individual differences in dietary motivation and providing targeted recommendations and strategies. In this review, we first present an overview of the interaction between diet, host genetics, and gut microbiota and collected some latest research associated with microRNAs modulated gut microbiota and intestinal homeostasis. Then, specifically described the possible molecular mechanisms of microRNAs in sensing and regulating gut microbiota-host crosstalk. Lastly, summarized the prospect of microRNAs as biomarkers in disease diagnosis, and the disadvantages of microRNAs in regulating gut microbiota-host crosstalk. We speculated that microRNAs could become potential novel circulating biomarkers for personalized dietary strategies to achieve precise nutrition in future clinical research implications.

Anti-inflammatory and antioxidant activities of methanol extract of Piper betle Linn. (Piper betle L.) leaves and stems by inhibiting NF-κB/MAPK/Nrf2 signaling pathways in RAW 264.7 macrophages

Oxidative stress and chronic inflammation are closely linked to various diseases. However, previous studies have demonstrated that plant extracts could prevent and alleviate these adverse outcomes. Piper betle Linn. (Piper betle L.) is a cosmopolitan plant that belongs to the Piperaceae family, whose leaves are edible and possess several health benefits. This study sought to characterize the anti-inflammatory and antioxidant effects of a methanol extract of Piper betle L. leaves and stems (MPBLLS). MPBLLS was found to have a dose-dependent radical scavenging effect, as demonstrated by the 2,2-diphenyl-1-picrylhydrazyl assay. Additionally, MPBLLS inhibited the lipopolysaccharide (LPS)-stimulated production of nitric oxide and prostaglandin E₂ by reducing the expression of inducible nitric oxide synthase and cyclooxygenase-2 in RAW 264.7 macrophages without affecting cell viability. Furthermore, our findings suggested that the inhibitory effects of MPBLLS on pro-inflammatory cytokines such as tumor necrosis factor-α, interleukin-1β, and interleukin-6 were due to the inhibition of the nuclear factor-κB (NF-κB) and mitogen-activated protein kinase (MAPK) signaling pathways in LPS-treated RAW 264.7 macrophages. MPBLLS and hydroxychavicol, a major constituent of MPBLLS, suppressed LPS-induced translocation of NF-κB p65 from cytoplasm to nucleus. Interestingly, MPBLLS increased nuclear factor erythroid 2-related factor 2 (Nrf2) protein levels and transcription levels of Nrf2 target genes in a dose-dependent manner. Collectively, our findings suggest that MPBLLS could serve as a basis for the development of novel orally-administered therapies due to its inhibitory effects on oxidative and inflammatory stress. DATA AVAILABILITY: The data presented in this study are available on request from the corresponding author.

Environmental Pollutants and Oxidative Stress in Terrestrial and Aquatic Organisms: Examination of the Total Picture and Implications for Human Health

There is current great international concern about the contribution of environmental pollution to the global burden of disease particularly in the developing, low- and medium-income countries. Industrial activities, urbanization, developmental projects as well as various increased anthropogenic activities involving the improper generation, management and disposal of pollutants have rendered today's environment highly polluted with various pollutants. These pollutants include toxic metals (lead, cadmium, mercury, arsenic), polycyclic aromatic hydrocarbons, polychlorinated biphenyls, pesticides and diesel exhaust particles most of which appear to be ubiquitous as well as have long-term environmental persistence with a wide range of toxicities such as oxidative stress among others. Oxidative stress, which may arise from increased production of damaging free radicals emanating from increased pollutant burden and depressed bioavailability of antioxidant defenses causes altered biochemical and physiological mechanisms and has been implicated in all known human pathologies most of which are chronic. Oxidative stress also affects both flora and fauna and plants are very important components of the terrestrial environment and significant contributors of nutrients for both man and animals. It is also remarkable that the aquatic environment in which sea animals and creatures are resident is also highly polluted, leading to aquatic stress that may affect the survival of the aquatic animals, sharing in the oxidative stress. These altered terrestrial and aquatic environments have an overarching effect on human health. Antioxidants neutralize the damaging free radicals thus, they play important protective roles in the onset, progression and severity of the unmitigated generation of pollutants that ultimately manifest as oxidative stress. Consequently, human health as well as that of aquatic and terrestrial organisms may be protected from environmental pollution by mitigating oxidative stress and employing the principles of nutritional medicine, essentially based on antioxidants derived mainly from plants, which serve as the panacea of the vicious state of environmental pollutants consequently, the health of the population. Understanding the total picture of oxidative stress and integrating the terrestrial and aquatic effects of environmental pollutants are central to sustainable health of the population and appear to require multi-sectoral collaborations from diverse disciplinary perspectives; basically the environmental, agricultural and health sectors.

Nutrigenomics and Nutrigenetics Research in New Zealand, and Its Relevance and Application to Gastrointestinal Health

Nutrigenomics New Zealand (NuNZ) was a collaborative research programme built among three organisations-the University of Auckland, AgResearch Limited and Plant & Food Research. The programme ran for ten years, between 2004 and 2014, and was tasked with developing the then emerging field of nutrigenomics, investigating its applications to New Zealand, and potential benefits to the plant food and agricultural sectors. Since the beginning of the programme, nutrigenomics was divided into two fields-nutrigenetics and nutrigenomics. The first of these is now more commonly called personalised nutrition, and has recently been recognised and criticised by elements of the dietetics and management sector in New Zealand, who currently do not appear to fully appreciate the evolving nature of the field, and the differing validity of various companies offering the tests that form the basis of this personalisation. Various science laboratories are utilising "omics" sciences, including transcriptomics, metabolomics, proteomics and the comprehensive analysis of microbial communities such as the gut microbiota, in order to understand the mechanisms by which certain food products and/or diets relevant to New Zealand, confer a health benefit, and the nature of potential health claims that may be made on the basis of this information. In this article, we give a brief overview of the nutrigenomics landscape in New Zealand since the end of the NuNZ programme, with a particular focus on gastrointestinal health.

Utilizing the underutilized plant resources for development of life style foods: Putting nutrigenomics to use

Sufficient amount of minerals, vitamins, and proteins in human diet play indispensable role in maintaining the active metabolism for better human health. All the essential nutrients that are requisite for an individual's survival are acquired from plants as well as animals. Micronutrients and macronutrients directly influence the metabolic pathways and their deficiencies play a substantial role in development of manifold disorders. In addition to environmental factors, quality and quantity of foods are key factors in maintaining the human health. Transition from healthy to diseased state is concurrent with the pattern of gene expression that is largely influenced by nutrition and environment. A combined approach to study the influence of nutrition on expression of numerous genes can be well explored through nutrigenomic studies. Nutrigenomics includes studies wherein applied genomics is used to investigate nutritional science to understand the compartmentalization of genes that influence the cause of diet-related complications. This review describes the role of underutilized crops as frontline foods to circumvent the health complications through the nutrigenomic studies. Further dynamics of nutrigenomic tools to study the impact of nutrition on the changing pattern of genome stability and gene expression for developing precise safety measures against wide range of health ailments linked to metabolic networks. Additionally, this review provides detailed information on nutrigenomic studies undertaken to unravel the potential of underutilized crops to augment the human health and to carry the agronomic/genomic approaches to enhance nutritional profile of underutilized crops to overcome diet-related disorders.

Genes Related to Fat Metabolism in Pigs and Intramuscular Fat Content of Pork: A Focus on Nutrigenetics and Nutrigenomics

Simple Summary

The intramuscular fat (IMF) or marbling is an essential pork sensory quality that influences the preference of the consumers and premiums for pork. IMF is the streak of visible fat intermixed with the lean within a muscle fibre and determines sensorial qualities of pork such as flavour, tenderness and juiciness. Fat metabolism and IMF development are controlled by dietary nutrients, genes, and their metabolic pathways in the pig. Nutrigenetics explains how the genetic make-up of an individual pig influences the pig’s response to dietary nutrient intake. Differently, nutrigenomics is the analysis of how the entire genome of an individual pig is affected by dietary nutrient intake. The knowledge of nutrigenetics and nutrigenomics, when harmonized, is a powerful tool in estimating nutrient requirements for swine and programming dietary nutrient supply according to an individual pig’s genetic make-up. The current paper aimed to highlight the roles of nutrigenetics and nutrigenomics in elucidating the underlying mechanisms of fat metabolism and IMF deposition in pigs. This knowledge is essential in redefining nutritional intervention for swine production and the improvement of some economically important traits such as growth performance, backfat thickness, IMF accretion, disease resistance etc., in animals.

Abstract

Fat metabolism and intramuscular fat (IMF) are qualitative traits in pigs whose development are influenced by several genes and metabolic pathways. Nutrigenetics and nutrigenomics offer prospects in estimating nutrients required by a pig. Application of these emerging fields in nutritional science provides an opportunity for matching nutrients based on the genetic make-up of the pig for trait improvements. Today, integration of high throughput “omics” technologies into nutritional genomic research has revealed many quantitative trait loci (QTLs) and single nucleotide polymorphisms (SNPs) for the mutation(s) of key genes directly or indirectly involved in fat metabolism and IMF deposition in pigs. Nutrient–gene interaction and the underlying molecular mechanisms involved in fatty acid synthesis and marbling in pigs is difficult to unravel. While existing knowledge on QTLs and SNPs of genes related to fat metabolism and IMF development is yet to be harmonized, the scientific explanations behind the nature of the existing correlation between the nutrients, the genes and the environment remain unclear, being inconclusive or lacking precision. This paper aimed to: (1) discuss nutrigenetics, nutrigenomics and epigenetic mechanisms controlling fat metabolism and IMF accretion in pigs; (2) highlight the potentials of these concepts in pig nutritional programming and research.

Influence of the Bioactive Diet Components on the Gene Expression Regulation

Diet bioactive components, in the concept of nutrigenetics and nutrigenomics, consist of food constituents, which can transfer information from the external environment and influence gene expression in the cell and thus the function of the whole organism. It is crucial to regard food not only as the source of energy and basic nutriments, crucial for living and organism development, but also as the factor influencing health/disease, biochemical mechanisms, and activation of biochemical pathways. Bioactive components of the diet regulate gene expression through changes in the chromatin structure (including DNA methylation and histone modification), non-coding RNA, activation of transcription factors by signalling cascades, or direct ligand binding to the nuclear receptors. Analysis of interactions between diet components and human genome structure and gene activity is a modern approach that will help to better understand these relations and will allow designing dietary guidances, which can help maintain good health.

Contribution of genetic ancestry and polygenic risk score in meeting vitamin B12 needs in healthy Brazilian children and adolescents

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.

Dietary vegetable oils inclusion on the performance, hormonal levels and hsp 70 gene expression in broilers under heat stress

The aim of the present study was to compare the effects of unsaturated and saturated oils on the performance, hormonal levels and hsp gene expression in broiler chickens exposed to heat stress. 300 one-day male broiler chicks were assigned to 4 treatments (Diets containing palm, corn, linseed or olive oils) with 5 replicates. At day 28 of age, 2 chickens were removed from each replicate, then blood samples and liver tissue samples were collected for analyses. Feeding linseed and olive oil reduced feed conversion ratio compared to corn and palm oils. The lowest level of insulin was for chickens fed linseed oil and corn oil. The highest level of corticosterone was found in chickens fed palm oil and the lowest level was for those received linseed oil. Chickens received linseed and corn oils had the highest levels of T3 and T4 and those fed palm and olive oils had the lowest levels. The highest HSP 70 gene expression was for chickens fed diet containing olive and linseed oils and the lowest one was for those fed corn and palm oils. It was concluded that olive oil and linseed oil could improve performance and heat tolerance of chickens under heat stress.

A Nutrigenomics Approach Using RNA Sequencing Technology to Study Nutrient-Gene Interactions in Agricultural Animals

Thorough understanding of animal gene expression driven by dietary nutrients can be regarded as a bottom line of advanced animal nutrition research. Nutrigenomics (including transcriptomics) studies the effects of dietary nutrients on cellular gene expression and, ultimately, phenotypic changes in living organisms. Transcriptomics can be applied to investigate animal tissue transcriptomes at a defined nutritional state, which can provide a holistic view of intracellular RNA expression. As a novel transcriptomics approach, RNA sequencing (RNA-Seq) technology can monitor all gene expressions simultaneously in response to dietary intervention. The principle and history of RNA-Seq are briefly reviewed, and its 3 principal steps are described in this article. Application of RNA-Seq in different areas of animal nutrition research is summarized. Lastly, the application of RNA-Seq in swine science and nutrition is also reviewed. In short, RNA-Seq holds significant potential to be employed for better understanding the nutrient-gene interactions in agricultural animals.

Use of dietary indices to control for diet in human gut microbiota studies

BACKGROUND

Environmental factors have a large influence on the composition of the human gut microbiota. One of the most influential and well-studied is host diet. To assess and interpret the impact of non-dietary factors on the gut microbiota, we endeavoured to determine the most appropriate method to summarise community variation attributable to dietary effects. Dietary habits are multidimensional with internal correlations. This complexity can be simplified by using dietary indices that quantify dietary variance in a single measure and offer a means of controlling for diet in microbiota studies. However, to date, the applicability of different dietary indices to gut microbiota studies has not been assessed. Here, we use food frequency questionnaire (FFQ) data from members of the TwinsUK cohort to create three different dietary measures applicable in western-diet populations: The Healthy Eating Index (HEI), the Mediterranean Diet Score (MDS) and the Healthy Food Diversity index (HFD-Index). We validate and compare these three indices to determine which best summarises dietary influences on gut microbiota composition.

RESULTS

All three indices were independently validated using established measures of health, and all were significantly associated with microbiota measures; the HEI had the highest t values in models of alpha diversity measures, and had the highest number of associations with microbial taxa. Beta diversity analyses showed the HEI explained the greatest variance of microbiota composition. In paired tests between twins discordant for dietary index score, the HEI was associated with the greatest variation of taxa and twin dissimilarity.

CONCLUSIONS

We find that the HEI explains the most variance in, and has the strongest association with, gut microbiota composition in a western (UK) population, suggesting that it may be the best summary measure to capture gut microbiota variance attributable to habitual diet in comparable populations.

Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men

The metabolic health benefits of fermented milks have already been investigated using clinical biomarkers but the development of transcriptomic analytics in blood offers an alternative approach that may help to sensitively characterise such effects. We aimed to assess the effects of probiotic yoghurt intake, compared to non-fermented, acidified milk intake, on clinical biomarkers and gene expression in peripheral blood. To this end, a randomised, crossover study was conducted in fourteen healthy, young men to test the two dairy products. For a subset of seven subjects, RNA sequencing was used to measure gene expression in blood collected during postprandial tests and after two weeks daily intake. We found that the postprandial response in insulin was different for probiotic yoghurt as compared to that of acidified milk. Moreover changes in several clinical biomarkers were associated with changes in the expression of genes representing six metabolic genesets. Assessment of the postprandial effects of each dairy product on gene expression by geneset enrichment analysis revealed significant, similar modulation of inflammatory and glycolytic genes after both probiotic yoghurt and acidified milk intake, although distinct kinetic characteristics of the modulation differentiated the dairy products. The aryl hydrocarbon receptor was a major contributor to the down-regulation of the inflammatory genesets and was also positively associated with changes in circulating insulin at 2h after yoghurt intake (p = 0.05). Daily intake of the dairy products showed little effect on the fasting blood transcriptome. Probiotic yoghurt and acidified milk appear to affect similar gene pathways during the postprandial phase but differences in the timing and the extent of this modulation may lead to different physiological consequences. The functional relevance of these differences in gene expression is supported by their associations with circulating biomarkers.

Recognition of phenylthiocarbamide (PTC) in taste test is related to blood group B phenotype, females, and risk of developing food allergy: a cross-sectional Brazilian-based study

Anti-nutritional factors, including hemagglutinins, are natural substances that reduce nutritional bioavailability and/or generate adverse physiological effects. Most are bitter toxic compounds, but present chemo-protective properties at low concentrations. Responses to phenylthiocarbamide (PTC) allow for an evaluation of humans' perception of bitter taste, a perception that has evolutionary advantages. Therefore, we hypothesized that relationships between food preference, dietary exposures and disease risk could reflect possible associations not only with the recognition threshold for the bitter taste of PTC, but also with ABO/Rh blood group phenotypes. To test this hypothesis, 375 volunteers of both genders, aged 16-49 years, were recruited. Data were obtained from laboratory tests and questionnaires. PTC test followed literature; blood typing used commercially available sera. Allele frequencies calculated from phenotypes were: T=0.51, t=0.49 (PTC); I^A=0.22, I^B=0.08, i=0.70 (ABO); D=0.57, d=0.43 (Rh). Associations with the recognition threshold for bitter taste were found for blood group B, females, and risk of developing food allergy for bitter taste at PTC dilution 1 (the highest concentration) (OR=3.862; 95%CI=1.387-10.756; p=0.016); for each more diluted PTC solution, the chance of food allergy fell 25.2% (95%CI = 0.764-0.836), while for each more concentrated solution the chance of food allergy increased 20.1% (p=0.000). There were also nominally significant differences among PTC tasting, ABO/Rh, genders and age-groups in relation to food preferences. Results demonstrated that the ability to recognize PTC in taste test is related to blood group B, females, and risk of developing food allergy, thus confirming the research hypothesis, and presenting original and important associations.

Protective Role of Co-administration of Vitamin D in Monosodium Glutamate Induced Obesity in Female Rats

PURPOSE

Obesity in females is an emerging health problem. The consumption of MSG has been considered as a risk factor for obesity. The tastemakers in Chinese and fast foods, such as fish sauce and soy sauce, contain very high levels of glutamate. The deficiency of Vitamin D is associated with obesity and metabolic syndrome. Therefore, the present study aimed to determine the effect of co-administration of Vitamin D on body weight control in MSG-induced obese rats.

METHODS

Eighteen adult female Wistar rats were randomly divided into three groups equally. The first group (Group I) was treated with saline served as the control; the second group (Group II) received a daily oral dose of 5 g/kg Body weight of MSG; the third group (Group III) received the same dose of MSG along with calcitriol (0.2 mcg/kg BW) for 15 days.

RESULTS

The body weight, food, and water intake were measured. MSG treated rats showed a significant increase (P < 0.001) in the body weight, food, and water intake but significant decrease (P < 0.001) was observed in the rats treated with MSG along with Vitamin D.

CONCLUSION

Ingestion of Vitamin D suppresses body weight gain in MSG-induced obese rats. Active agents in Vitamin D are useful for the prevention and treatment of obesity. Foods tested with high glutamate levels can be fortified with minute quantities of calcitriol to combat the adverse effects without compromising on the taste of the food processed. The fortification of junk foods might also combat largely prevalent Vitamin D deficiency in India.

Oregano dietary supplementation modifies the liver transcriptome profile in broilers: RNASeq analysis

Intensive farming of broilers involves stressful conditions that reduce animal welfare and performance. New dietary strategies to improve performance and meat quality include the administration of plant extracts. Oregano (Origanum vulgare L.) is known for its antimicrobial, anti-fungal, insecticidal and antioxidant properties. However, studies on diet supplementation with oregano are mainly focused on the evaluation of animal performance, while partial information is available on transcriptomics and nutrigenomics and, in particular, Next Generation Sequencing (NGS) is not widely applied. In this study we tested the effect of an oregano aqueous extract supplemented diet on gene expression in broiler chickens. Whole liver transcriptome of 10 birds fed with a supplemented diet versus 10 controls was analyzed using the RNA-Seq technique. One hundred and twenty-nine genes were differentially expressed with an absolute log fold change >1. The analysis reveals a massive down-regulation of genes involved in fatty acid metabolism and insulin signaling pathways in broilers fed with the oregano aqueous extract supplementation. Down-regulated genes could be associated to chicken lean line, suggesting the potential beneficial effect of oregano supplementation in reducing both abdominal and visceral fat deposition. Down-regulation of insulin signaling pathway related genes suggest that dietary oregano supplementation might be an option in obesity and diabetes conditions.

Informatics for Nutritional Genetics and Genomics

While traditional nutrition science is focusing on nourishing population, modern nutrition is aiming at benefiting individual people. The goal of modern nutritional research is to promote health, prevent diseases, and improve performance. With the development of modern technologies like bioinformatics, metabolomics, and molecular genetics, this goal is becoming more attainable. In this chapter, we will discuss the new concepts and technologies especially in informatics and molecular genetics and genomics, and how they have been implemented to change the nutrition science and lead to the emergence of new branches like nutrigenomics, nutrigenetics, and nutritional metabolomics.

Propelling the paradigm shift from reductionism to systems nutrition

The complex physiology of living organisms represents a challenge for mechanistic understanding of the action of dietary bioactives in the human body and of their possible role in health and disease. Animal, cell, and microbial models have been extensively used to address questions that could not be pursued experimentally in humans, posing an additional level of complexity in translation of the results to healthy and diseased metabolism. The past few decades have witnessed a surge in development of increasingly sensitive molecular techniques and bioinformatic tools for storing, managing, and analyzing increasingly large datasets. Application of such powerful means to molecular nutrition research led to a major leap in study designs and experimental approaches yielding experimental data connecting dietary components to human health. Scientific journals bear major responsibilities in the advancement of science. As primary actors of dissemination to the scientific community, journals can impose rigid criteria for publishing only sound, reliable, and reproducible data. Journal policies are meant to guide potential authors to adopt the most updated standardization guidelines and shared best practices. Such policies evolve in parallel with the evolution of novel approaches and emerging challenges and therefore require constant updating. We highlight in this manuscript the major scientific issues that led to formulating new, updated journal policies for Genes & Nutrition, a journal which targets the growing field of nutritional systems biology interfacing personalized nutrition and preventive medicine, with the ultimate goal of promoting health and preventing or treating disease. We focus here on relevant issues requiring standardization in nutrition research. We also introduce new sections on human genetic variation and nutritional bioinformatics which follow the evolution of nutritional science into the twenty-first century.

Mediterranean diet-gene interactions: A targeted metabolomics study in Greek-Cypriot women

SCOPE

A high adherence to the Mediterranean diet (MD) was previously associated with a decreased risk of breast cancer (BC) among Greek-Cypriot women. Additionally, particular polymorphisms were shown to modulate this MD-BC association. Herein, we aimed to investigate the effect of polymorphisms-MD interactions on the levels of specific metabolites that could be related to dietary adherence or enzymatic activity, which is itself modulated by polymorphisms.

METHODS AND RESULTS

Greek-Cypriot women who were BC controls and had the lowest or the highest MD adherence (vegetables, fruit, legumes, fish) as assessed by principal component analysis (n = 564) were included. Participants were previously genotyped for nine polymorphisms of the one-carbon metabolism, oxidative stress, and xenobiotic metabolism. The serum levels of 14 metabolites that are key players in the aforementioned pathways were measured by UPLC-MS/MS. ANCOVA was used to assess polymorphism-MD interactions on metabolites' levels within a multivariate linear regression model. Statistically significant interactions between GSTM1 (where GST is glutathione S-transferase) deletion polymorphism and MD on flavin mononucleotide and on 5-methyltetrahydrofolate (5-MTHF) concentrations were observed. The MTHFR rs1801133 interacted significantly with MD on 5-MTHF concentration.

CONCLUSION

Serum levels of flavin mononucleotide and 5-MTHF were shown to be influenced by interactions between GSTM1 deletion or MTHFR (rs1801133) polymorphisms and a dietary pattern, characteristic of MD.

Proteome changes in the small intestinal mucosa of growing pigs with dietary supplementation of non-starch polysaccharide enzymes

Background

Non-starch polysaccharide enzymes (NSPEs) have long been used in monogastric animal feed production to degrade non-starch polysaccharides (NSPs) to oligosaccharides in order to promote growth performance and gastrointestinal (GI) tract health. However, the precise molecular mechanism of NSPEs in the improvement of the mammalian small intestine remains unknown.

Methods

In this study, isobaric tags were applied to investigate alterations of the small intestinal mucosa proteome of growing pigs after 50 days of supplementation with 0.6% NSPEs (mixture of xylanase, β-glucanase and cellulose) in the diet. Bioinformatics analysis including gene ontology annotation was performed to determine the differentially expressed proteins. A protein fold-change of ≥ 1.2 and a P-value of < 0.05 were selected as thresholds.

Results

Dietary supplementation of NSPEs improved the growth performance of growing pigs. Most importantly, a total of 90 proteins were found to be differentially abundant in the small intestinal mucosa between a control group and the NSPE group. Up-regulated proteins were related to nutrient metabolism (energy, lipids, protein and mineral), immunity, redox homeostasis, detoxification and the cell cytoskeleton. Down-regulated proteins were primarily related to transcriptional and translational regulation. Our results indicate that the effect of NSPEs on the increase of nutrient availability in the intestinal lumen facilitates the efficiency of nutrient absorption and utilization, and the supplementation of NSPEs in growing pigs also modulates redox homeostasis and enhances immune response during simulating energy metabolism due to a higher uptake of nutrients in the small intestine.

Conclusions

These findings have important implications for understanding the mechanisms of NSPEs on the small intestine of pigs, which provides new information for the better utilization of this feed additive in the future.

Electronic supplementary material

The online version of this article (doi:10.1186/s12953-016-0109-6) contains supplementary material, which is available to authorized users.

Nutrigenomics and its Impact on Life Style Associated Metabolic Diseases

Post-human genome revelation observes the emergence of 'Nutigenomics' as one of the exciting scientific advancement influencing mankind around the world. Food or more precisely 'nutrition' has the major impact in defining the cause-response interaction between nutrient (diet) and human health. In addition to substantial understanding of nutrition-human-health interaction, bases of 'nutrigenomic' development foster on advent in transcriptomics, genomics, proteomics and metabolomics as well as insight into food as health supplement. Interaction of selected nutrient with associated genes in specific organ or tissue necessary to comprehend that how individual's genetic makeup (DNA transcribed into mRNA and then to proteins) respond to particular nutrient. It provided new opportunities to incorporate natural bioactive compounds into food for specific group of people with similar genotype. As inception of diabetes associated with change in gene expression of, not limited to, protein kinase B, insulin receptor, duodenal homeobox and glucokinase, thus, targeting such proteins by modifying or improving the nutritional availability or uptake may help to devise novel food, supplements, or nutraceuticals. In this article, various aspects of R&D in nutrigenomics are reviewed to ascertain its impact on human health, especially with life-style associated diseases.

Modeling-Enabled Systems Nutritional Immunology

This review highlights the fundamental role of nutrition in the maintenance of health, the immune response, and disease prevention. Emerging global mechanistic insights in the field of nutritional immunology cannot be gained through reductionist methods alone or by analyzing a single nutrient at a time. We propose to investigate nutritional immunology as a massively interacting system of interconnected multistage and multiscale networks that encompass hidden mechanisms by which nutrition, microbiome, metabolism, genetic predisposition, and the immune system interact to delineate health and disease. The review sets an unconventional path to apply complex science methodologies to nutritional immunology research, discovery, and development through “use cases” centered around the impact of nutrition on the gut microbiome and immune responses. Our systems nutritional immunology analyses, which include modeling and informatics methodologies in combination with pre-clinical and clinical studies, have the potential to discover emerging systems-wide properties at the interface of the immune system, nutrition, microbiome, and metabolism.

The genomics of micronutrient requirements

Healthy nutrition is accepted as a cornerstone of public health strategies for reducing the risk of noncommunicable conditions such as obesity, cardiovascular disease, and related morbidities. However, many research studies continue to focus on single or at most a few factors that may elicit a metabolic effect. These reductionist approaches resulted in: (1) exaggerated claims for nutrition as a cure or prevention of disease; (2) the wide use of empirically based dietary regimens, as if one fits all; and (3) frequent disappointment of consumers, patients, and healthcare providers about the real impact nutrition can make on medicine and health. Multiple factors including environment, host and microbiome genetics, social context, the chemical form of the nutrient, its (bio)availability, and chemical and metabolic interactions among nutrients all interact to result in nutrient requirement and in health outcomes. Advances in laboratory methodologies, especially in analytical and separation techniques, are making the chemical dissection of foods and their availability in physiological tissues possible in an unprecedented manner. These omics technologies have opened opportunities for extending knowledge of micronutrients and of their metabolic and endocrine roles. While these technologies are crucial, more holistic approaches to the analysis of physiology and environment, novel experimental designs, and more sophisticated computational methods are needed to advance our understanding of how nutrition influences health of individuals.

Approaches for the identification of genetic modifiers of nutrient dependent phenotypes: examples from folate

By combining the sciences of nutrition, bioinformatics, genomics, population genetics, and epidemiology, nutrigenomics is improving our understanding of how diet and nutrient intake can interact with or modify gene expression and disease risk. In this review, we explore various approaches to examine gene–nutrient interactions and the modifying role of nutrient consumption, as they relate to nutrient status and disease risk in human populations. Two common approaches include the use of SNPs in candidate genes to identify their association with nutritional status or disease outcomes, or genome-wide association studies to identify genetic polymorphisms associated with a given phenotype. Here, we examine the results of various gene–nutrient interaction studies, the association of genetic polymorphisms with disease expression, and the identification of nutritional factors that modify gene-dependent disease phenotypes. We have focused on specific examples from investigations of the interactions of folate, B-vitamin consumption, and polymorphisms in the genes of B-vitamin dependent enzymes and their association with disease risk, followed by an examination of the strengths and limitations of the methods employed. We also present suggestions for future studies, including an approach from an on-going large scale study, to examine the interaction of nutrient intake and genotypic variation and their impact on nutritional status.

Genetic associations with micronutrient levels identified in immune and gastrointestinal networks

The discovery of vitamins and clarification of their role in preventing frank essential nutrient deficiencies occurred in the early 1900s. Much vitamin research has understandably focused on public health and the effects of single nutrients to alleviate acute conditions. The physiological processes for maintaining health, however, are complex systems that depend upon interactions between multiple nutrients, environmental factors, and genetic makeup. To analyze the relationship between these factors and nutritional health, data were obtained from an observational, community-based participatory research program of children and teens (age 6–14) enrolled in a summer day camp in the Delta region of Arkansas. Assessments of erythrocyte S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH), plasma homocysteine (Hcy) and 6 organic micronutrients (retinol, 25-hydroxy vitamin D3, pyridoxal, thiamin, riboflavin, and vitamin E), and 1,129 plasma proteins were performed at 3 time points in each of 2 years. Genetic makeup was analyzed with 1 M SNP genotyping arrays, and nutrient status was assessed with 24-h dietary intake questionnaires. A pattern of metabolites (met_PC1) that included the ratio of erythrocyte SAM/SAH, Hcy, and 5 vitamins were identified by principal component analysis. Met_PC1 levels were significantly associated with (1) single-nucleotide polymorphisms, (2) levels of plasma proteins, and (3) multilocus genotypes coding for gastrointestinal and immune functions, as identified in a global network of metabolic/protein–protein interactions. Subsequent mining of data from curated pathway, network, and genome-wide association studies identified genetic and functional relationships that may be explained by gene–nutrient interactions. The systems nutrition strategy described here has thus associated a multivariate metabolite pattern in blood with genes involved in immune and gastrointestinal functions.

The influence of erythropoietin (EPO T → G) and α-actinin-3 (ACTN3 R577X) polymorphisms on runners' responses to the dietary ingestion of antioxidant supplementation based on pequi oil ( Caryocar brasiliense Camb.): a before-after study

BACKGROUND/AIMS

As diet can affect an individual's genes and these can affect response to supplementation, we aimed to investigate the influence of erythropoietin (EPO T→G) and α-actinin-3 (ACTN3 R577X) polymorphisms on plasma lipid peroxidation, hemogram and biochemical dosages of creatine kinase, aspartate aminotransferase, alanine aminotransferase and C-reactive protein (including high-sensitivity C-reactive protein) of runners (n = 123) before and after 14 days of 400 mg pequi oil supplementation, a natural carotenoid-rich oil, after races under closely comparable conditions.

METHODS/RESULTS

Blood samples were taken immediately after racing to perform the tests. Before pequi oil supplementation, EPO polymorphism influenced erythrogram and plateletgram results, suggesting an aerobic advantage for the TG genotype and a disadvantage for the GG genotype as regards possible microvascular complications, while no association was found for ACTN3 polymorphism with endurance performance. Both polymorphisms influenced the runners' response to pequi oil: significant responses were observed for the EPO TT genotype in erythrocyte, hematocrit, mean corpuscular hemoglobin and mean corpuscular hemoglobin concentration values, and for the TT and TG genotypes in red blood cell distribution width values. Significant differences were also observed in the plateletgram for the TT and TG genotypes. ACTN3 mainly influenced aspartate aminotransferase and creatine kinase values: heterozygotes had a significant reduction in aspartate aminotransferase values and homozygous individuals (XX) in creatine kinase values after pequi oil supplementation.

CONCLUSION

These results emphasize the importance of studying nutrigenomic effects on athletes' performance.

Sulforaphane: translational research from laboratory bench to clinic

Cruciferous vegetables are widely acknowledged to provide chemopreventive benefits in humans, but they are not generally consumed at levels that effect significant change in biomarkers of health. Because consumers have embraced the notion that dietary supplements may prevent disease, this review considers whether an appropriately validated sulforaphane-yielding broccoli sprout supplement may deliver clinical benefit. The crucifer-derived bioactive phytochemical sulforaphane is a significant inducer of nuclear factor erythroid 2-related factor 2 (Nrf2), the transcription factor that activates the cell's endogenous defenses via a battery of cytoprotective genes. For a broccoli sprout supplement to demonstrate bioactivity in vivo, it must retain both the sulforaphane-yielding precursor compound, glucoraphanin, and the activity of glucoraphanin's intrinsic myrosinase enzyme. Many broccoli sprout supplements are myrosinase inactive, but current labeling does not reflect this. For the benefit of clinicians and consumers, this review summarizes the findings of in vitro studies and clinical trials, interpreting them in the context of clinical relevance. Standardization of sulforaphane nomenclature and assay protocols will be necessary to remove inconsistency and ambiguity in the labeling of currently available broccoli sprout products.

Signal transduction disturbance related to hepatocarcinogenesis in mouse by prolonged exposure to Nanjing drinking water

Toxicogenomic approaches were used to investigate the potential hepatocarcinogenic effects on mice by oral exposure to Nanjing drinking water (NJDW). Changes in the hepatic transcriptome of 3 weeks male mice (Mus musculus) were monitored and dissected after oral exposure to NJDW for 90 days. No preneoplastic and neoplastic lesions were observed in the hepatic tissue by the end of NJDW exposure. However, total of 746 genes were changed transcriptionally. Thirty-one percent of differentially expressed genes (DEGs) were associated with the functional categories of cell cycle regulation, adhesion, growth, apoptosis, and signal transduction, which are closely implicated in tumorigenesis and progression. Interrogation of Kyoto Encyclopedia of Genes and Genomes revealed that 43 DEGs were mapped to several crucial signaling pathways implicated in the pathogenesis of hepatocellular carcinoma (HCC). In signal transduction network constructed via Genes2Networks software, Egfr, Akt1, Atf2, Ctnnb1, Hras, Mapk1, Smad2, and Ccnd1 were hubs. Direct gene-disease relationships obtained from Comparative Toxicogenomics Database and scientific literatures revealed that the hubs have direct mechanism or biomarker relationships with hepatocellular preneoplastic lesions or hepatocarcinogenesis. Therefore, prolonged intake of NJDW without employing any indoor water treatment strategy might predispose mouse to HCC. Furthermore, Egfr, Akt1, Ctnnb1, Hras, Mapk1, Smad2, and Ccnd1 were identified as promising biomarkers of the potential combined hepatocarcinogenicity.

Iron deficiency modifies gene expression variation induced by augmented hypoxia sensing

In congenital Chuvash polycythemia (CP), VHL(R200W) homozygosity leads to elevated hypoxia inducible factor (HIF) levels at normoxia. CP is often treated by phlebotomy resulting in iron deficiency, permitting us to examine the separate and synergistic effects of iron deficiency and HIF signaling on gene expression. We compared peripheral blood mononuclear cell gene expression profiles of eight VHL(R200W) homozygotes with 17 wildtype individuals with normal iron status and found 812 up-regulated and 2120 down-regulated genes at false discovery rate of 0.05. Among differential genes we identified three major gene regulation modules involving induction of innate immune responses, alteration of carbohydrate and lipid metabolism, and down-regulation of cell proliferation, stress-induced apoptosis and T-cell activation. These observations suggest molecular mechanisms for previous observations in CP of lower blood sugar without increased insulin and low oncogenic potential. Studies including 16 additional VHL(R200W) homozygotes with low ferritin indicated that iron deficiency enhanced the induction effect of VHL(R200W) for 50 genes including hemoglobin synthesis loci but suppressed the effect for 107 genes enriched for HIF-2 targets. This pattern is consistent with potentiation of HIF-1α protein stability by iron deficiency but a trend for down-regulation of HIF-2α translation by iron deficiency overriding an increase in HIF-2α protein stability.

Oestradiol differentially influences feeding behaviour depending on diet composition in female rhesus monkeys

In females, cyclical changes in the ovarian hormone oestradiol are known to modulate feeding behaviour. However, what is less clear is how these behavioural effects of oestradiol are modified by the macronutrient content of a diet. In the present study, we report data showing that oestradiol treatment results in both significantly smaller meals and a reduced total calorie intake in ovariectomised, socially-housed female rhesus macaques when only chow diet is available. Conversely, during a choice dietary condition where both palatable and chow options are available, oestradiol treatment had no observable, attenuating effect on calorie intake. During this choice dietary phase, all animals consumed more of the palatable diet than chow diet; however, oestradiol treatment appeared to further increase preference for the palatable diet. Finally, oestradiol treatment increased snacking behaviour (i.e. the consumption of calories outside of empirically defined meals), regardless of diet condition. These findings illustrate how oestradiol differentially influences feeding behaviour depending on the dietary environment and provides a framework in which we can begin to examine the mechanisms underlying these observed changes.

Protective effects of a novel sea buckthorn wine on oxidative stress and hypercholesterolemia

We developed a novel sea buckthorn wine containing significant in vitro free radical-scavenging activity. High-performance liquid chromatographic analysis of the sea buckthorn wine revealed that it contains high rutin, myricetin and quercetin levels compared to Cabernet Shiraz wine. In this study, we evaluated the protective effects of sea buckthorn wine against phorone-induced oxidative stress and high-cholesterol diet induced hypercholesterolemia in male LACA mice. Oral administration of sea buckthorn wine increased the redox ratio accompanied by reduction of oxidized glutathione levels leading to attenuation of phorone-induced oxidative stress. Furthermore, the sea buckthorn wine supplementation reduced hepatic lipid peroxidation and increased the superoxide dismutase activity indicating improved resistance to oxidative stress. In addition, high-cholesterol-fed mice administered with sea buckthorn wine exhibited a 197% increase in the HDL-C/LDL-C ratio compared to high-cholesterol diet treated mice. These studies provide important evidence that sea buckthorn wine exerts protective effects against oxidative stress and hypercholesterolemia.