Personalized nutrition: Translating research to solutions

Epigenetics, advances in metabolomics and sequencing of the microbiome are among the scientific discoveries identified as most pertinent to the evolution of personalized nutrition.

Rachel French

February 13, 2019

12 Min Read
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“The realization that our genes are not our destiny is one of the greatest scientific discoveries of our generation,” said Jennifer Cooper, chief scientific officer at Savant Science, of epigenetics—the study of any process that alters gene expression without changing the DNA sequence.

“For most of us, that means that good health comes down to our own choices,” she continued. “It gives us hope that we don’t have to accept mediocre wellness outcomes, but also makes us responsible for making those changes a reality.” 

Epigenetics is among four scientific discoveries Cooper identified as most pertinent to the evolution of personalized nutrition.

The power of epigenetics and, thus, nutrigenomics (the study of the effects of nutrients/bioactives on gene expression) is rooted in the intricacy of genes. Though the genetic makeup of all people is 99 percent identical, genes have plasticity and can experience variations known as single nucleotide polymorphisms (SNPs). SNPs are responsible for the differences from person to person and can impact various processes within the body.

As explained by Amanda Archibald, R.D., The Genomic Kitchen, at SupplySide West 2018 during the Personalized Nutrition Workshop, genomic medicine looks at the collective number of SNPs in a biochemical pathway and assesses the impact of the total number of SNPs on physiological processes in the body.

“We can then use food and/or supplementation to influence the behavior of the gene,” she said.

Lois Nahirney, Ph.D., president and CEO, dnaPower, a Canada-based DNA health testing lab, also cited epigenetics a critical area of discovery in personalized nutrition. dnaPower, like most DNA testing labs, tests for genetics—“your DNA code,” Nahirney explained. A genetic test can identify genetic predispositions to certain diseases and genetic variations that can impact nutrition.

“Epigenetics is the layer that is on top of [the DNA code],” Nahirney explained. “Epigenetics is things like diet and nutrition and supplements, is exercise, activity, sleep, stress and environmental toxins. Those factors will impact how your DNA responds.”

Cooper referred to the impact of epigenetics as a “paradigm shift” from “the all-knowing physician to the empowered patient and all-questioning consumer. Now that we have taken our health into our own hands, there is an urgent need for the coalescing of scientifically sound information, data management and personalized health care to be crafted into integrated, consumer-friendly solutions.”

Researchers, health-conscious consumers and forward-thinking brands in the health and nutrition space are on the same page, and eagerly anticipating the health care revolution personalized nutrition and precision medicine can bring once fully realized.

Until then, steady advancements in research and technologies, along with ongoing innovation, is bringing various solutions to market. These solutions often involve retrieving input from consumers via genetic analysis, microbiome analysis, blood testing, questionnaires or activity trackers and then providing actionable insight or solutions—sometimes in the form of food delivery or supplement delivery services.

In the supplements category, the face of personalization continues to evolve. Currently, personalized supplementation may feature customized supplement subscriptions based on consumer feedback, supplements customized to dietary and lifestyle preferences, such as paleo, ketogenic or vegetarian diets and others.

Encouraging is the growth potential for supplements within the personalized nutrition market. According to market data from Wise Guy Reports, the personalized nutrition trend will push growth of vitamins, minerals and supplements at a compound annual growth rate (CAGR) of 6.5 percent from an estimated total value of US$93 billion in 2015 to $127 billion in 2020.

Further supporting growth of supplements within the personalized nutrition category is expanding research, which continues to unlock the potential of personalized nutrition and nutrient intake on individual health outcomes.

Beyond epigenetics, exciting areas of research, per Cooper, include sequencing of the microbiome, advances in metabolomics and bioinformatics as a discipline.


Researchers continue their quest to understand the microbiome and its potential impact on health. Early findings uncovered links between the microbiome and certain health disorders, such as obesity,1 insulin resistance,2 type 2 diabetes,3 glucose intolerance,4 non-alcoholic fatty liver disease 5 and others.

Recent findings, however, strive to understand the microbiome’s potential in precision medicine and personalized nutrition, largely inspired by the discovery of vast variability of the microbiome on an individual basis.

“When scientists started sequencing the microbiome, we expected to find a core group of organisms that were basically common in humans regardless of the culture, food consumption, environmental exposure, age and world location,” Cooper said. “Surprisingly, they found that more than 80 percent of an individual’s biome is unique. While they didn’t always find the same core group of organisms, they found the same core group of functions were reliably carried out by a healthy person’s microbiome.”

She continued, “The inherent variability in individual microbiomes and its impact on everything from [gastrointestinal] function, immunity, brain function, metabolism and drug pharmacokinetics means that better understanding this complex, symbiotic, ‘other’ organ will have a profound impact on both personalized nutrition and precision medicine.”

Zmora N et al. agreed in a 2016 publication,: “At present, microbiome research is moving beyond description of community structure and disease associations, toward a deeper molecular understanding of its contributions to the pathogenesis of complex disorders. As such, recent next-generation DNA sequencing-based studies are suggesting that the utilization of person-specific microbiome data may contribute to the development of precision medicine, personalized diagnostic and treatment modalities.”6

Among research demonstrating how variations in the microbiome impact health outcomes related to diet is a study reviewing the gut microbiota metabolism of L-carnitine, a nutrient abundant in red meat.7 Metabolism of L-carnitine by the intestinal microbiota produces trimethylamine-N-oxide (TMAO), linked to acceleration of atherosclerosis—hardening of the arteries and a leading cause of heart disease. Chronic dietary L-carnitine supplementation in mice significantly altered fecal microbial composition, markedly enhanced synthesis of TMAO, and increased atherosclerosis, but not following suppression of intestinal microbiota. Further, the study reported omnivorous subjects are shown to produce significantly more TMAO than vegans/vegetarians following ingestion of L-carnitine through a microbiota-dependent mechanism.

Commenting on the study, Zmora et al. wrote, “This suggests that global recommendation to reduce consumption of red meat as a means of reducing cardiovascular diseases may be more relevant for people with specific microbiome configurations, calling for personalized adjustment of universal recommendations.”

Another study evaluated the potential of non-caloric artificial sweeteners (NAS) to induce glucose intolerance.8 Researchers found consumption of commonly used NAS formulations drive the development of glucose intolerance through induction of compositional and functional alterations to the intestinal microbiota. Based on the findings, Zmora et al. suggested “recommendations for the reduction of sugar consumption via the widespread use of NAS may be harmful to some population subsets and that we might need to personalize this recommendation according to the individual’s microbiome.”

Research further demonstrated the impact of diet on the microbiome.

Long-term diets are strongly associated with enterotypes distinguished primarily by levels of Bacteroides (protein and animal fat) and Prevotella (carbohydrates).9 Though initiation of a high-fat/low-fiber or low-fat/high-fiber diet caused a detectable change of the microbiome within 24 hours, the participants’ enterotype identities remained stable during the 10-day, controlled-feeding study, suggesting alternative enterotype states are associated with a long-term diet.

Another study found similar results, noting differences in the microbiome occurred after only a single day on a strictly animal-based diet, and the microbiome of these individuals reverted to its normal state two days after the animal-based diet ended.10 A plant-based diet was also shown to have a significant effect on the microbiome.

Applying technology is another step toward realizing the potential of recent scientific discoveries.

In a 2018 review by Bashiardes S et al., authors said, “The inclusion of the microbiome as a necessary element explaining personal uniqueness has led to a paradigm shift in terms of our understanding of inter-individual variability and how it influences responses to environmental factors (such as diet). We are now in an era where we finally have the technologies that allow us to devise data-driven approaches to personalized diet interventions that take into account variation at the level of our genome and microbiome.”11

The review cited a 2015 study by Zeevi et al. that continuously monitored week-long glucose levels in an 800-person cohort, measured responses to 46,898 meals and found high variability in the response to identical meals.12 Researchers devised a machine-learning algorithm that integrates blood parameters, dietary habits, anthropometrics, physical activity and gut microbiota measured in the cohort and showed that it accurately predicts personalized postprandial glycemic response to real-life meals. The predictions were validated in an independent 100-person cohort. Finally, a blinded, randomized, controlled dietary intervention based on this algorithm resulted in significantly lower postprandial responses and consistent alterations to gut microbiota configuration.

Commenting on the findings, Bashiardes S et al. wrote, “Authors developed a revolutionary algorithm for predicting postprandial glucose responses by integrating microbiome composition, blood tests and antropometrics of 1,000 people. This is the first study that utilizes a machine learning approach and microbiome information for personally tailored diet intervention.”

As noted by Zmora et al., the microbiome’ has great potential to positively impact health. “The microbiome is readily modifiable, potentially allowing for not only the detection and risk stratification of individuals at risk for disease, but also their comprehensive follow-up and reevaluation,” the authors wrote. “With the automation of microbiome analysis, such longitudinal microbiome-based follow up may become accessible and cost-effective even at local community settings.”

However, the authors also indicated challenges: “The microbiome is modified by both host nutrition and its own metabolic state and in turn regulates the host metabolic homeostasis. As such, personalized nutritional interventions must take into account these intricate and bilateral relationships between the microbiome and host, which may be ‘reset’ to a new steady state by longstanding personalized nutritional modifications.”


Metabolomics is the study of chemical processes involving metabolites, the intermediate end product of metabolism.

Metabolomics is also an area of rapid scientific development, according to Cooper.

“Our ability to track changes in genetic expression via lifestyle choices has been dependent upon correlating those changes against diaries kept by subjects on food consumption, estimates on toxin exposure, sleep variation and other lifestyle factors,” she explained, adding that these data, even when collected in a clinical setting, “are notorious for inadequacies and errors.” She cited a common example: Subjects who estimate too low on food consumption and too high on hours of sleep.

“We are looking for nuances in genetic expression using very sophisticated tools against imprecisely measured changes in diet and environmental exposure using archaic and inaccurate methods.”

Metabolomics, she said, has the potential to make good such clinical faux pas.

“The science of metabolomics is going to solve all of these quandaries and exponentially advance its sister sciences of epigenetics, personalized nutrition and precision medicine,” she said. “Instead of asking you what you ate, we are going to be able to look at a massive number of new biomarkers and tell you what you ate with great precision.”

And developments are already underway. In the past, Cooper said routine testing evaluated roughly 30 biomarkers.

“Today, laboratory testing is available to most people that can test about 300 of the 800 biomarkers we have identified. Tomorrow there will be more than 100,000 metabolites identified, not counting thousands more that are the products of our microbiome bacterial metabolism,” she said.    

Additionally, researchers suggested a need for greater understanding of the molecular composition of food. Authors of a Journal of Nutrigenetics and Nutrigenomics publication explained: “With the advent of metabolomics, foods and beverages are now being analyzed with considerably more chemical detail, and thousands of chemical entities are being detected or identified in certain foods.”13 Called the “food metabolome,” this collection of food components, “could provide a piece of critical information for the study of complex interactions between nutrition and health.”

Driving Solutions Forward

Despite recent discoveries and advancements, many uncertainties in the world of personalized nutrition remain, one of them being: how to create effective, personalized solutions.

But uncertainty, Cooper said, is no reason to withdraw. “If you are overwhelmed with the logistics of DNA, fecal microbiome or metabolome testing, or if you are stymied by the development of your own proprietary self-quantification device, you should not abandon the concept of personalized nutrition,” she advised.

Instead, companies can take “baby steps” toward personalized nutrition to speak to consumers on a more personalized level. “Even if the product is for ‘everyone,’ it needs to be described to each consumer in terms of why it is specifically for them and might include: specialized content, targeted messaging, personalized dosing instructions, unique dosage vehicles, lifestyle advice and integration with other health platforms and/or self-quantification devices and the management of big data.”

She cited other potential approaches to personalized nutrition, including:

  • Systems biology/physiological capacity for adaptation

  • Artificial Intelligence (AI)

  • Lifestyle recommendations: specialized diets, recipes, customized exercise programs, stress management, sleep modulation, tools for stopping bad habits and adopting good habits, mediated community support and personalized counselling or coaching, etc.

  • Personalized packaging solutions

  • Delivery mechanisms

  • Chronobiological considerations

  • Testing: DNA, biomarkers (metabolome), microbiome, etc.

  • Unique manufacturing schematics

  • Behavior modification

  • Improved adherence motivators

  • Diagnostic tools

  • Self-monitoring: devices, apps, consumer data

Looking forward, one clear conclusion about the future of personalized nutrition is it’s going to change.

“The progress we’ve made in nutrigenomics is phenomenal, and there’s a lot of information that can help now, but there is a wealth of new information still to be had,” Nahirney said. Topics such as compliance, technological integration, epigenetics, bioinformatics and more will see continued interest and development, driving forward the reality of personalized nutrition.


  1. Duranti S et al. “Obesity and microbiota: an example of an intricate relationship.” Genes Nutr. 2017;12:18.

  2. Le Chatelier E et al. “Richness of human gut microbiome correlates with metabolic markers.” Nature. 2013;500:541–546.

  3. Qin J et al. “A metagenome-wide association study of gut microbiota in type 2 diabetes.” Nature. 2012;490:55–60.

  4. Zhang X et al. “Human gut microbiota changes reveal the progression of glucose intolerance.” PLoS ONE. 2013:e71108.

  5. Yan AW et al. “Enteric dysbiosis associated with a mouse model of alcoholic liver disease.” Hepatology. 2011;53:96–10

  6. Zmora N et al. “Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease.” Cell Host & Microbe. 2016;19:12-20.

  7. Koeth RA et al. “Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis.” Nat Med. 2013;19:576–585.

  8. Suez J et al. “Artificial sweeteners induce glucose intolerance by altering the gut microbiota.” Nature. 2014;514:181–186.

  9. Wu GD et al. “Linking longterm dietary patterns with gut microbial enterotypes.” Science. 2011;334:105–108.

  10. David LA et al. “Diet rapidly and reproducibly alters the human gut microbiome.” Nature. 2014;505:559–563.

  11. Bashiardes S et al. “Towards utilization of the human genome.” Current Opinion in Biotechnology. 2018;51:57-63.

  12. Zeevi D et al. “Personalized Nutrition by Prediction of Glycemic Responses.” Cell. 2015 Nov 19;163(5):1079-1094.

  13. Astarita G, Langridge J. “An Emerging Role for Metabolomics in Nutrition Science.” J Nutrigenet Nutrigenmoics. 2013;6:181-200.



About the Author(s)

Rachel French

Rachel French joined Informa’s Health & Nutrition Network in 2013. Her career in the natural products industry started with a food and beverage focus before transitioning into her role as managing editor of Natural Products Insider, where she covered the dietary supplement industry. French left Informa Markets in 2019, but continues to freelance for both FBI and NPI.

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