Nutrigenomics: Personalizing Nutrition Through Your DNA

By: Isis Lee, volunteer and student at the University of Toronto, reviewed by Doug Cook, RD, and the JM Nutrition Team

 

Nutrigenomics: Introduction

Standard food guides and recommendations have shaped nutrition education for decades in order to reduce risk of disease across broad populations. While these guidelines provide a useful foundation, they often fail to explain or accommodate outliers: individuals who follow the same advice but experience vastly different health outcomes.

Advances in genetics and molecular biology have begun to explain a long-standing problem in nutrition. We now understand that identical dietary patterns can lead to different outcomes because of our fundamental biological differences. Each person has their own unique metabolism influenced by their DNA, and even the smallest genetic variation can affect how nutrients are digested, absorbed, transported and utilized in the body (Park 2025).

Nutrigenomics is the field that studies these interactions between diet and genes. It examines how naturally occurring genetic variations can alter a person’s response to specific nutrients and how dietary components can influence gene expression and metabolic pathways (Kassem et al. 2023).

In this post, we will explore how small genetic differences can change the way the body processes nutrients, look at emerging research on how food influences gene activity, and explain why nutritional science is moving beyond “one-size-fits-all” advice toward a more personalized approach.

 

Nutritional genomics: Exploring how food and genes interact

Nutritional genomics seeks to map the molecular landscape where diet and genes intersect. To navigate this relationship, interactions are typically viewed in two complementary directions: how our genetic variations affect the way nutrients are absorbed and utilized, and how nutrients themselves act within our cells to regulate gene activity. While these terms are used interchangeably, “nutritional genomics” is the umbrella term that involves both Nutrigenetics and Nutrigenomics reflecting the reciprocal relationship between genetic code and dietary signals (Ahluwalia 2021).

Nutrigenetics: How genes influence nutrient response

Nutrigenetics is the study of how your genes influence the way your body responds to the foods you eat. Although all humans are roughly 99.9% genetically identical, the remaining 0.1% includes small genetic variations, sometimes as simple as a single letter change in your DNA. These tiny differences can affect how your body processes food and uses the nutrients in your diet.

These variations can affect nutrient metabolism in several ways:

Enzyme activity: Reduces how well the enzyme binds to a nutrient which slows the conversion rate of a vitamin into its active form.

Transport efficiency: Changes to nutrient transport proteins can reduce the body’s ability to move nutrients across cell membranes. As a result, even if a person eats enough of a nutrient, their cells may not absorb or use it properly, which can lead to deficiencies.

Receptor sensitivity: Differences in nutrient receptors can affect how well cells recognize and respond to nutrients in the bloodstream. If these receptors don’t work as efficiently, the body may not use certain nutrients as effectively.

Together, these genetic factors help determine the bioavailability and efficacy of the foods you consume.

 

Here are some of the most researched examples of how specific genes affect nutrient metabolism and dietary response:

Satiety and FTO gene

FTO gene short for “fat mass and obesity associated” regulates appetite and energy balance. Individuals carrying the risk variant often experience higher levels of the hunger hormone ghrelin, blunting satiety response which can lead to increased food intake and reduce feelings of fullness.

However, FTO status does not guarantee obesity and can be managed through target nutrition. Research suggests that high protein diets are effective for this genotype as protein can suppress ghrelin and trigger satiety, while prioritizing unsaturated fats and regular physical activity can further dampen the gene’s influence on body mass (Hess and Brüning 2014).

Caffeine and CYP1A2 gene

CYP1A2 gene is responsible for producing the primary enzyme that determines how fast you metabolize and clear caffeine. Fast metabolizers process caffeine quickly, which provides a temporary performance-enhancing effect followed by efficient clearance.

However, for slow metabolizers, caffeine remains in the bloodstream significantly longer which heightens sensitivity and acts as a prolonged stressor on the cardiovascular system and central nervous system. Research shows that slow metabolizers who consume more than two cups of coffee daily may face increased risk of hypertension and heart palpitations (Kazan et al. 2024). People who are slow metabolizers are advised to limit caffeine intake to early hours and stay under the 200mg daily intake to protect heart health and sleep quality.

Lactose intolerance and LCT

The LCT gene provides instructions for producing lactase, the enzyme needed to break down the lactose sugar in dairy. While most humans naturally decrease LCT gene expression and stop producing lactase after infancy which is what causes lactose intolerance in adulthood, certain populations have instead developed lactose persistence and can produce the enzyme throughout adulthood (Cohen et al. 2024). Understanding your LCT gene status can help explain digestive symptoms and guide dairy consumption. Those with reduced lactase production can choose lactose-free alternatives, dairy products with lower lactose or take lactase supplements when consuming traditional dairy.

 

Benefits of Nutrigenomics

There exist a number of benefits of nutrigenomics.

1. Increased Adherence 

A major challenge in the field of nutritional counselling is the tendency for individuals to lose motivation when following generic advice. Multiple studies have shown that when presented with DNA-based evidence advice, participants had significantly greater and more sustained improvements in their dietary habits (Horne et al. 2020; Aljasir et al. 2024). By offering clearer and more personalized advice, nutrigenomics eliminates guesswork and helps individuals stay committed to their health goals.

2. Early intervention and disease prevention

Traditionally, dietary changes are made after symptoms such as high blood pressure or high cholesterol levels become apparent. By the time these markers are detected, underlying physiological stress has likely been developing for years. Nutrigenomics allows us to be proactive in detecting disease and predicting risk.

3. Identify Confounders for nutritional research

One of the most significant academic contributions of nutrigenomics is the ability to explain the inconsistent findings frequently observed in  nutrition research. For years, dietary studies have produced contradictory conclusions which are reflected in conflicting headlines such as coffee being associated with cardiovascular benefit in one study and increased risk of heart attack in another.

Nutrigenomics reveals that the mixed results are often caused by hidden genetic distribution of study participants. When researchers reanalyzed caffeine studies and separated participants into fast and slow metabolizers of the CYP1A2, the outcomes became more consistent. Caffeine intake was protective for fast metabolizers while slow metabolizers exhibited increased cardiovascular risk.

By identifying and accounting for genetic confounders, nutrigenomics allows for a more nuanced interpretation of nutritional data and highlights that the same nutrient may be beneficial for one individual and a physiological stressor for another.

 

Challenges and current limitations within nutrigenomics

Despite its potential, nutrigenomics is still an emerging science. Therefore, it is important to approach genetic testing with a realistic perspective on current constraints.

Polygenic traits

Most health outcomes are not the result of a single gene, but rather are polygenic where hundreds of genes interact simultaneously.

Genetics vs Environment gap

Genetics only provides a blueprint, but your lifestyle such as sleep, exercise and stress are exposures that influence gene expression. A genetic risk indicates susceptibility, not a predetermined outcome.

Cost and accessibility

While direct to consumer genetic tests have become more affordable, comprehensive analysis and professional interpretation can still be cost prohibitive for many individuals. Insurance coverage for nutrigenomics testing remains limited.

Regulation and Ethical concerns

As the direct to consumer testing market grows, there are concerns regarding data privacy and the accuracy of interpretations vary wildly between different companies.

There is a glaring conflict of interest when the same company performing the DNA test is also the one selling proprietary supplement. This creates financial incentive to over-recommend or exaggerate the severity of a genetic variant to ensure a recurring monthly subscription. Legitimate nutrigenomics should focus on food interventions first and use supplements only as a temporary target bridge.

 

Future applications

We are moving forward where a DNA test is just the starting line. In the next decade, we expect several key developments:

Multi-Omics approach

Advancing towards personalized nutrition requires looking beyond isolated DNA markers. To comprehensively profile an individual’s biological state, researchers employ a multiomics approach that examines the Transcriptome (gene expression), Proteome (protein production and activity) and metabolome (metabolic byproducts). Integrating these layers reveals how nutrition actively interacts and affects each person’s biology in real time.

Microbiome-genome

Emerging research reveals that gut bacteria can actively influence how nutrients are metabolized and which genes are expressed. Unlike inherited DNA, gut bacterial composition can be shifted through dietary intervention, probiotic supplementation or lifestyle changes. Future applications will likely include microbiome profiling alongside genetic testing, with practitioners recommending specific prebiotics, probiotics or dietary patterns designed to optimize your microbial ecosystem based on your genetic vulnerabilities (Kasseem et al. 2023).

Integration of AI and personalization

As datasets grow larger and more comprehensive, artificial intelligence will help identify complex patterns and gene-diet-environment interactions that would be difficult for humans to detect manually. Machine learning algorithms can synthesize genetic data, health history, lifestyle factors and real-time biomarkers to generate increasingly precise dietary recommendations.

 

Nutrigenomics: Final Thoughts

Nutrigenomics does not replace the fundamentals of nutrition. Whole foods, hydration and dietary balance still matter, but it provides the fine-tuning needed to move beyond generalized recommendations and toward individualized advice. By understanding our own genetic makeup, we stop fighting against our biology and start working with it. 

There is no single “perfect diet” that works for everyone. What promotes health in one person may contribute to disease risk in another, depending on the intricate interplay between genes, nutrients, and environment, Nutrigenomics offers a framework for understanding these individual differences and translating them into actionable dietary strategies. 

As science continues to evolve, the gap between what we eat and who we are will only continue to close, bridging the gap between genetic predisposition and dietary intervention.

 

Conclusion

Should you feel you require personalized sessions for guidance around nutrigenomics and related matters, book a free consultation or contact us for an appointment. As always if you have comments or questions, we encourage you to let us know.

 

References

Ahluwalia MK. 2021. Nutrigenetics and nutrigenomics-A personalized approach to nutrition. Advances in Genetics. 108:277–340. doi: https://doi.org/10.1016/bs.adgen.2021.08.005. [accessed 2022 May 31]. https://pubmed.ncbi.nlm.nih.gov/34844714/.

Aljasir S, Eid NMS, Volpi EV, Tewfik I. 2024. Nutrigenomics-guided lifestyle intervention programmes: A critical scoping review with directions for future research. Clinical Nutrition ESPEN. 64:296–306. doi: https://doi.org/10.1016/j.clnesp.2024.10.149. https://www.sciencedirect.com/science/article/pii/S2405457724014876?via%3Dihub.

Cohen CE, Swallow DM, Walker C. 2024. The molecular basis of lactase persistence: Linking genetics and epigenetics. Annals of Human Genetics. 89(5). doi: https://doi.org/10.1111/ahg.12575.

Hess ME, Brüning JC. 2014. The fat mass and obesity-associated (FTO) gene: Obesity and beyond? Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease. 1842(10):2039–2047. doi: https://doi.org/10.1016/j.bbadis.2014.01.017. https://www.sciencedirect.com/science/article/pii/S0925443914000337.

Horne J, Gilliland J, O’Connor C, Seabrook J, Madill J. 2020. Enhanced long-term dietary change and adherence in a nutrigenomics-guided lifestyle intervention compared to a population-based (GLB/DPP) lifestyle intervention for weight management: results from the NOW randomised controlled trial. BMJ Nutrition, Prevention & Health. 3(1):49–59. doi: https://doi.org/10.1136/bmjnph-2020-000073.

Kassem NM, Abdelmegid YA, El-Sayed MK, Sayed RS, Abdel-Aalla MH, Kassem HA. 2023. Nutrigenomics and microbiome shaping the future of personalized medicine: a review article. Journal of Genetic Engineering and Biotechnology. 21(1):134–134. doi: https://doi.org/10.1186/s43141-023-00599-2.

Kazan HH, Celal Bulgay, Ercan Zorba, Metin Dalip, Ceylan Hİ, Semenova EA, Larin AK, Kulemin NA, Generozov EV, Ahmetov II, et al. 2024. Exploring the relationship between caffeine metabolism-related CYP1A2 rs762551 polymorphism and team sport athlete status and training adaptations. Molecular Biology Reports. 51(1). doi: https://doi.org/10.1007/s11033-024-09800-2.

Park S. 2025. Editorial: Precision nutrition and nutrients: making the promise a reality. Frontiers in Nutrition. 12. doi: https://doi.org/10.3389/fnut.2025.1553149.

 

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About Author:

Doug is a Toronto-based dietitian who provides nutritional support in the following areas: support for digestive health concerns, brain health, heart health support, healthy aging and more.

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