Metabolites produced by people, animals and plants during the process of building up and breaking down molecules are biomarkers of biochemical pathways, processes of health and disease and the effectiveness of interventions.
The study of these biomarkers, metabolomics, could deliver insights across food, metabolism and health, with potential wider impacts at scale across agriculture and preventing disease.
The ERA Chair Foodomics project is funded by the European Union under the Horizon Europe banner, and is exploring the pioneering field of metabolomics in relation to food and diet.
Bringing together leading departments of the University of Ljubljana and a network of distinguished research institutions and stakeholders across Slovenia, the project is hosted by the Biotechnical Faculty, specifically its Department of Food Science and Technology, in collaboration with the Department of Agronomy and Department of Animal Science.
Additionally, the project integrates expertise from the Faculty of Medicine and the Faculty of Mathematics and Physics at the University of Ljubljana.
The project aims to establish a dedicated research centre. A dynamic and sustainable state-of-the-art research environment will solidify Slovenia’s strategic position as a hub of excellence for innovation in food science, offering research opportunities, potentially patentable discoveries and strengthen the Slovenian and wider European economies.
Metabolomics offers unprecedented insights into nutrition, the gut microbiome and our health.
One of the few guarantees in today’s world is that everyone needs to eat. But new research and technical innovations are constantly shaping how we approach food.
Studies of metabolomics in food science have revealed new depths to the gut microbiome, enabling nutritionists to better understand the impact of ultra processed foods, respond to disease and even meet the needs of specific ‘metabotypes’.
Metabolomics provides a vital framework for evaluating the nutritional, functional and safety aspects of emerging foods, which can help make food systems more sustainable, either by optimising existing foodstuffs or identifying suitable alternatives.
Artificial intelligence (AI) is used to analyse the swathes of valuable data metabolomics offers, enabling more efficient study and research.
The Innovation News Network spoke with ERA Chair Coordinator Professor Nataša Poklar Ulrih to learn more.
In my view, metabolomics will become one of the most transformative technologies in nutrition and health because it allows us to connect food, metabolism and health in ways that were not previously possible. Rather than focusing solely on nutrients, we can better understand how foods interact with biological systems and influence health throughout life.
By measuring thousands of small molecules in foods and biological samples, metabolomics provides a real-time snapshot of biological and physiological status.
Its most immediate impact will be in personalised nutrition, early disease detection and precision prevention. Metabolic signatures reflecting dietary habits, lifestyle, environmental exposures and health status can help tailor nutritional recommendations to individual needs and identify disease risk before clinical symptoms appear. Metabolic biomarkers can also provide objective measures of dietary intake and intervention effectiveness.
Beyond healthcare, metabolomics has important applications in food quality, authenticity and safety.
It can help detect food fraud, contaminants, natural toxins and processing effects, supporting regulatory agencies and consumer confidence.
Metabolomics is also becoming a key tool for sustainable food production and climate resilience.
It helps researchers understand how drought, heat stress and other environmental pressures affect crop quality and nutritional value, supporting the development of climate-resilient crops. In parallel, it enables comprehensive evaluation of plant-based foods, alternative proteins, precision-fermentation products and other emerging food sources.
Another exciting area is the study of diet-microbiome interactions. Many health benefits of foods are mediated by microbial metabolites, and understanding these pathways may open new opportunities for disease prevention and personalised nutrition.
Looking ahead, the integration of metabolomics with artificial intelligence, genomics, microbiome science and digital health technologies could enable a more predictive approach to healthcare. Instead of reacting to disease, we may be able to identify early metabolic changes and intervene through targeted dietary and lifestyle strategies.
What excites me most is that metabolomics connects the entire food-health continuum, from crop production and food processing to individual metabolic responses and disease risk. I believe this systems-level perspective will be essential for addressing some of society’s greatest challenges, including chronic disease prevention, healthy ageing, food security and climate resilience.
What makes metabolomics particularly powerful is that it reflects the combined effects of genes, environment, diet and the microbiome at a given moment. In many ways, it provides a molecular snapshot of how an individual is functioning rather than what we might predict from genetics alone.
For example, two individuals may consume an identical meal yet show markedly different responses in blood glucose, lipid metabolism, inflammatory markers or satiety signals. By analysing thousands of metabolites before and after food consumption, researchers can identify the biochemical pathways responsible for these differences and gain insight into how the body processes nutrients.
This approach helps define individual metabolic profiles and can reveal characteristics that are not apparent from genetic or clinical data alone. Combined with microbiome and lifestyle information, metabolomics is enabling the development of more personalised nutrition strategies that account for biological individuality. Ultimately, this knowledge may allow dietary recommendations to be tailored to maximise health benefits, improve disease prevention and support long-term wellbeing for each person.
Metabotypes are groups of individuals who share similar metabolic characteristics, regardless of age, sex or other traditional classifications. They reflect how a person’s body processes nutrients, regulates metabolism and responds to environmental and lifestyle factors. Identifying these metabolic phenotypes is becoming an important step towards precision nutrition.
Current dietary guidelines are largely designed for populations and often assume that individuals will respond similarly to the same nutritional advice.
However, growing evidence suggests that people with different metabolic profiles may have very different responses to identical diets. For example, individuals with metabolic signatures associated with insulin resistance, altered lipid metabolism, chronic inflammation or impaired microbial metabolism may benefit from distinct dietary interventions compared with metabolically healthy individuals.
Metabolomics provides the tools needed to identify these metabotypes by measuring a wide range of metabolites that reflect underlying biological processes. This information may eventually allow healthcare professionals to classify individuals according to their metabolic needs and provide more targeted nutritional recommendations.
In the future, nutrition advice may be based not only on age or body weight but also on metabolic phenotype, leading to more effective dietary interventions, improved disease prevention and better health outcomes. Such approaches have the potential to move nutrition science from general recommendations towards truly personalised dietary guidance.
Accurately measuring what people eat remains one of the biggest challenges in nutrition research. Traditional dietary assessment methods, such as food frequency questionnaires, food diaries and dietary recalls, depend on self-reporting and are often affected by memory errors, underreporting and reporting bias.
Metabolomics offers an opportunity to complement and improve these methods through the identification of objective dietary biomarkers.
Over the past decade, substantial progress has been made in identifying biomarkers associated with specific foods and dietary patterns. Validated biomarkers already exist for foods such as coffee, citrus fruits, fish, whole grains, alcohol and several plant-based foods. These biomarkers provide measurable evidence of food intake and can help verify dietary adherence in nutritional studies. However, replacing dietary questionnaires entirely remains challenging because no single metabolite can capture the complexity of a complete diet.
The future is likely to involve combining traditional dietary assessment methods with metabolomics based biomarker panels. As analytical technologies improve, databases expand and validation studies are conducted across diverse populations, these biomarkers will become increasingly reliable. Ultimately, objective dietary biomarkers could significantly improve nutrition research, strengthen personalised nutrition approaches and provide healthcare professionals with more accurate tools for assessing dietary habits and monitoring nutritional interventions.
One of the most important discoveries in nutrition science has been that the gut microbiome acts as a metabolic organ, producing thousands of compounds that influence health. Trillions of microorganisms residing in the gastrointestinal tract continuously interact with dietary components and generate metabolites that affect immune function, metabolism and disease risk.
As a result, diet affects health not only through nutrients directly absorbed by the body but also through compounds generated by microbial, metabolism.
Research has shown that dietary patterns can rapidly alter the composition and metabolic activity of the gut microbiome. In turn, microbial metabolites can influence immune regulation, energy metabolism, inflammation, cardiovascular health and even brain function. Some of the most extensively studied examples include short-chain fatty acids, secondary bile acids and indole derivatives, all of which play important roles in host health.
One of the key discoveries has been that many of the health benefits associated with fibre-rich diets arise from microbial fermentation processes and the production of beneficial metabolites rather than from fibre alone. We also increasingly recognise the importance of human-microbial co-metabolism, where host and microbial pathways work together to influence health outcomes.
These findings are transforming nutrition science by shifting the focus from individual nutrients to dynamic interactions between food, microbes and metabolism. Understanding these interactions is essential for developing personalised nutrition strategies, improving disease prevention and promoting healthy ageing.
Microbial metabolites such as short-chain fatty acids (SCFAs), bile acids and indoles are receiving increasing attention because they act as key signalling molecules connecting diet, the gut microbiome and human health. Rather than being simple by-products of microbial activity, they act as molecular messengers that allow diet, microbes and human cells to communicate. Among these compounds, SCFAs, including acetate, propionate and butyrate, are produced when gut microbes ferment dietary fibres and other prebiotics. They help maintain intestinal barrier integrity, regulate immune function, reduce inflammation and support healthy glucose and lipid metabolism. Bile acids, which are modified by the gut microbiota, influence energy metabolism, appetite regulation and immune responses, while indoles, generated from microbial metabolism of dietary tryptophan, play important roles in gut barrier function and mucosal immunity.
From a Foodomics perspective, these metabolites are particularly valuable because they provide measurable links between food intake, microbiome activity and health outcomes. They are also considered important postbiotics, the biologically active compounds produced by microorganisms that mediate many of the beneficial effects associated with diet, prebiotics and probiotics. By quantifying these metabolites, metabolomics helps us understand how foods influence health, why individuals respond differently to the same diet and how nutritional interventions can be tailored more effectively. As a result, microbial metabolites are emerging both as biomarkers of health and as promising targets for personalised nutrition and disease prevention.
Metabolomics is transforming microbiome research by allowing scientists to move beyond identifying which microorganisms are present and instead understand their functional activity and impact on human health. Because metabolites are the end products of biological processes, they provide a direct measure of how diet influences interactions between the microbiome and the host.
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