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Your Guide to Metabolomics

Chapter 7—Commercial Applications of Metabolomics

In previous chapters of this guide, we explored the scientific discovery and breakthroughs enabled by metabolomics, from basic science research in the academic laboratory to clinical application and the growing future of precision medicine. In this chapter, we’ll see how metabolomics supports a range of commercial applications, from nutrition to beauty and everything in between.

Drug Development (Pre-clinical and Clinical)

While drug development relies on academic and clinical research, it isn’t solely a research venture. The ultimate goal, of course, is to obtain regulatory approval (eg, FDA, EMA) and manufacture the drug at scale to serve the medical community while, of course, making a profit. Metabolomics can support several arms of early drug discovery and development:1 identifying metabolites/biomarkers, identifying bioactive compounds, studying the metabolism of the compound, characterizing efficacy and toxicity of the compound. All of which are critical for establishing safety and efficacy of a drug and ultimately gaining FDA approval.

Metabolomics can also support the design of efficacious clinical trials and/or troubleshoot trials that are failing for unknown reasons. For example, Metabolon’s Global Discovery Panel was used to help develop a more efficacious dosing strategy and redesign of a clinical trial to bring a microbiome-based therapeutic that had failed Phase II clinical trials through a successful Phase III trial.2 The impact is considerable because, by the time drugs make it to later stages of clinical trials, hundreds of millions of dollars have already been spent on their development. Ensuring successful clinical trials can improve the success rate3 experienced by the pharmaceuticals industry today, ultimately lowering costs for everyone, including the patients who will be taking the drug.

Nutritional Sciences

Food and Drink Safety and Manufacturing

Most of us don’t give a second thought about where our food comes from or the processes it went through to get to us. We don’t wonder whether the piece of bread we’re about to eat has nutritional value or worry whether it’s safe to eat or contaminated with substances that could make us sick. We just eat. Metabolomics plays a crucial role in providing us the peace of mind to simply enjoy our food without having to think about it.

Industrial food and beverage production is a multifaceted process. Not only must flavor and nutritional profiles be upheld, but quality and health standards must also be met to avoid sickening the population. Metabolomics is a valuable tool used by the food and beverage industry4 to ensure flavor, quality, and safety:

  • Flavor: The taste of food is usually linked to primary and secondary non-volatile metabolites. Profiling these metabolites can provide valuable information about the flavor of food. For example, profiling the impact of marination5 on these metabolites in meat can reveal important impacts on flavor (and thus, consumer buying habits). Additionally, ensuring realistic taste is a major goal of the alternative meat/protein industry6 (including plant-based products); doing so can make major inroads to releasing humanely produced and environmentally friendly sources of protein on a global scale.
  • Quality: Metabolomics can quickly and easily profile markers of nutritional quality,4 including carotenoids, flavonoids, volatiles, and other metabolites. Tracking these markers over time can also inform strategies to preserve freshness and maximize shelf-life, as well as to identify issues in the supply chain that negatively impact food quality. Appearance can also be an indicator of quality to consumers; for example, the color of fresh meat7 (changes which can be characterized with metabolomics) is a major factor impacting consumers’ perception of meat quality.
  • Food safety: Metabolomics is often used to identify whether microbial toxins and other contaminants are present in food. Contaminants are not just limited to bacterial and fungal pathogens; researchers have also used metabolomics to profile the levels of veterinary drugs in raw milk,8 demonstrating the role of metabolomics tools in food safety in dairy processing specifically.

All of the categories described above can and are impacted by the processing of foods and beverages, which can include heating, mixing, and drying—so continued metabolic profiling of food throughout the entire production process9 can ensure the highest levels of flavor, quality, and safety.

Metabolomics can also play a crucial role in ensuring that food and beverage production companies adhere to regulatory standards,10 often around labeling. Production companies have been known to include false information about the origin, production, processing, and nutritional profile on their labels, switching out components for inferior ingredients to save money on the production of high-grade foods. Such fraudulent activities can be easily detected by metabolomics.11 Similarly, foods with “organic” labels can be tested for their adherence to guidelines required to market a food or food product as organic (which often comes with steeper prices at the grocery store).

Vitamins and Supplements Quality Control

As with food and beverages, the effects of vitamins and supplements—including potential toxicity—should be carefully characterized and monitored. Although interest in vitamins and supplements has increased substantially over the past 20 years, they still remain relatively understudied12 as a substance intended for human consumption, largely due to differences in classification, regulation, and even definition around the world. Metabolomics (as well as other omics techniques) have played an important role in characterizing the metabolic and physiological impact and toxicity of the most common supplements, vitamins D, E, and A, and plant extracts such as resveratrol, green tea, ginseng, and curcumin.

Plant-derived supplements are the fastest-growing segment12 of the supplements industry and face the biggest issues with quality control and standardization. To address this, researchers have proposed frameworks13 for the development of plant-derived/botanical supplements that mirror those of the typical pharmaceutical, both to ensure that the science around them is sound and reproducible and to ensure that safe and efficacious supplements are produced and released to the public. In the same way, metabolomics supports quality drug development, it can also support quality supplement development.

Similar to the food and beverage industry, metabolomics can also keep vitamin and supplement manufacturers accountable and honest by detecting inferior ingredients, contaminants, or fillers and by accurately tracking the source(s) of different substances to ensure that the products reaching the consumer are true-to-label and of high quality and purity.

Metabolomics studies of vitamins and supplements can also provide critical information for informing dosing, co-delivery with other vitamins, supplements, and drugs, and individualized responses to supplementation14 that could inform personalized approaches to supplementation. Vitamin D is the most well-studied vitamin12 in all of these aspects, but these studies lay the foundation for others investigating any vitamin or supplement.

Personal Care and Cosmetics

Cosmetics and other products developed for topical application can be medicinal (eg, skin-care products to treat acne), cosmetic (eg, makeup to cover up acne), or simply support good hygiene (eg, toothpaste). But regardless of their intended purpose, these products interact with and impact our skin, hair, mouth, and eyes, including the microbial communities that live in and on those body sites, and impact our health and well-being. Although studies are few compared to the food and supplement industries, researchers are beginning to unravel how cosmetic ingredients impact the human metabolome,15 for good or bad.

Metabolomics approaches are playing an increasingly important role in the responsible development of safe and effective personal care and cosmetics products. A leading multibillion-dollar cosmetics company leveraged Metabolon’s services to understand the natural circadian rhythm of skin, characterize deficiencies in this rhythm as skin ages, and develop skincare products targeting those deficiencies to improve skin health. Others are using metabolomics to research alternative ingredients (such as cannabinoids16) as potential replacements for existing products containing substances that may do more harm than good, including to our endocrine systems and the environment.

Safety assessment is also a significant component of cosmetics production. With animal testing banned or frowned upon (depending on each country’s regulatory standards), new methods leveraging metabolomics and in vitro assays17 can comprehensively analyze a substance’s impact on distribution, metabolism, and intracellular impacts.

What’s Next for Commercial Applications of Metabolomics?

In this chapter, we explored the myriad ways metabolomics supports and improves drug development, food and beverage production, and personal care and cosmetics development. We also introduced the role metabolomics can play in ensuring adherence to regulatory standards, specifically for foods and supplements. In the next chapter of this guide, we’ll discuss metabolomics and regulatory standards more broadly and in greater detail.

Continue to Chapter 8 - Regulatory Applications of Metabolomics

In the next chapter, we’ll explore the ways in which metabolomics can help define and uphold governmental and agency regulations and guidelines.


  1. Alarcon-Barrera JC, Kostidis S, Ondo-Mendez A et al. Recent advances in metabolomics analysis for early drug development. Drug Discov Today. 2022;27(6):1763–1773. doi:10.1016/j.drudis.2022.02.018
  2. McGovern BH, Ford CB, Henn MR, et al. SER-109, an Investigational Microbiome Drug to Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial. Clin Infect Dis. Jun 15 2021;72(12):2132-2140. doi:10.1093/cid/ciaa387
  3. Wong CH and Siah KW. Estimation of clinical trial success rates and related parameters. Biostatistics. 2019;20(2):273–286. doi: 10.1093/biostatistics/kxx069
  4. Pedrosa MC, Lima L, Heleno S et al. Food Metabolites as Tools for Authentication, Processing, and Nutritive Value Assessment. Foods. 2021;10(9):2213. doi: 10.3390/foods10092213
  5. Yang Y, Ye Y, Pan D et al. Metabonomics profiling of marinated meat in soy sauce during processing. J Sci Food Agric. 2018;98(4):1325–1331. doi: 10.1002/jsfa.8596
  6. Jacobs DM, van den Berg MA, and Hall RD. Towards superior plant-based foods using metabolomics. Curr Opin Biotechnol. 2021;70:23–28. doi: 0.1016/j.copbio.2020.08.010
  7. Wideman N, O’Bryan CA, and Crandall PG. Factors affecting poultry meat colour and consumer preferences – A review. World’s Poultry Sci Journal. 2015;353–366. doi:
  8. Zhan J, Yu XJ, Zhong YY et al. Generic and rapid determination of veterinary drug residues and other contaminants in raw milk by ultra performance liquid chromatography-tandem mass spectrometry. J Chromatogr B Anal Technol Biomed Life Sci. 2012;906:48–57. doi: 10.1016/j.jchromb.2012.08.018
  9. Kim S, Kim J, Yun EJ et al. Food metabolomics: from farm to human. Curr Opin Biotechnol. 2016;37:16–23. doi:
  10. Emwas AHM, Al-Rifai N, Szczepski K et al. You Are What You Eat: Application of Metabolomics Approaches to Advance Nutrition Research. Foods. 2021;10(6):1249. doi: 10.3390/foods10061249
  11. Wei F and Wu B. Chapter 3.05: Use of Lipidomics for Food Quality Assurance and Authentication. In: Cifuentes, A. Comprehensive Foodomics. Elsevier Inc. 2021;44–61. doi: 10.1016/B978-0-08-100596-5.22829-1
  12. Steg A, Oczkowicz M, and Smołucha G. Omics as a Tool to Help Determine the Effectiveness of Supplements. Nutrients. 2022;14(24):5305. doi: 10.3390/nu14245305
  13. van Breemen B. Development of Safe and Effective Botanical Dietary Supplements. J Med Chem. 2015;58(21):8360–8372. doi: 10.1021/acs.jmedchem.5b00417
  14. McClorry S, Slupsky CM, Lind T et al. Effectiveness of vitamin D supplementation in Swedish children may be negatively impacted by BMI and serum fructose. J Nutr Biochem. 2020;75:108251. doi: 10.1016/j.jnutbio.2019.108251
  15. Bouslimani A, da Silva R, Kosciolek T et al. The impact of skin care products on skin chemistry and microbiome dynamics. BMC Biology. 2019;17(1):47. doi: 10.1186/s12915-019-0660-6
  16. Aliferis K and Bernard-Perron D. Cannabinomics: Applications of Metabolomics in Cannabis (Cannabis sativa L.) Research and Development. Front Plant Sci. 2020;11:554. doi: 10.3389/fpls.2020.00554
  17. Jacques C, Jamin EL, Jouanin I et al. Safety assessment of cosmetics by read across applied to metabolomics data of in vitro skin and liver models. Arch Toxicol. 2021;85(10):3303–3322. doi: 10.1007/s00204-021-03136-7

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