When scientists cracked the human genome in 2003, many expected it would unlock the secrets of disease. However, genetics explained only about 10% of the risk, leaving the other 90% in the environment, with diet playing a huge part. Worldwide, poor diet is linked to around one in five deaths among adults aged 25 years or older, while in Europe, it accounts for nearly half of all cardiovascular deaths.

Despite decades of advice about cutting fat, salt, or sugar, obesity and diet-related illness have continued to rise. Clearly, something is missing from the way we think about food. For years, nutrition has often been framed in fairly simple terms: food as fuel and nutrients as the body’s building blocks. Proteins, carbohydrates, fats, and vitamins – about 150 known chemicals in total – have dominated the picture.

A New Perspective on Nutrition

However, scientists now estimate that our diet actually delivers more than 26,000 compounds, with most of them still uncharted. This phenomenon is often referred to as the ‘dark matter’ of nutrition, similar to the concept of dark matter in astronomy, which makes up about 27% of the universe but cannot be seen directly.

Some experts refer to these unknown molecules as ‘nutritional dark matter.’ It’s a reminder that just as the cosmos is filled with hidden forces, our diet is packed with hidden chemistry. When researchers analyze disease, they look at a vast array of foods, although any association often cannot be matched to known molecules.

This is the dark matter of nutrition – the compounds we ingest daily but haven’t been mapped or studied. Some may encourage health, but others may increase the risk of disease. The challenge is finding out which do what.

The Field of Foodomics

The field of foodomics aims to do exactly that. It brings together genomics (the role of genes), proteomics (proteins), metabolomics (cell activity), and nutrigenomics (the interaction of genes and diet). These approaches are starting to reveal how diet interacts with the body in ways far beyond calories and vitamins.

Take the Mediterranean diet, for example, which is known to reduce the risk of heart disease. But why does it work? One clue lies in a molecule called TMAO (trimethylamine N-oxide), produced when gut bacteria metabolize compounds in red meat and eggs. High levels of TMAO increase the risk of heart disease, but garlic, for example, contains substances that block its production.

This is one example of how diet can tip the balance between health and harm. Gut bacteria also play a major role. When compounds reach the colon, microbes transform them into new chemicals that can affect inflammation, immunity, and metabolism.

For example, ellagic acid – found in various fruits and nuts – is converted by gut bacteria into urolithins. These are a group of natural compounds that help keep our mitochondria (the body’s energy factories) healthy.

This shows how food is a complex web of interacting chemicals. One compound can influence many biological mechanisms, which in turn can affect many others. Diet can even switch genes on or off through epigenetics – changes in gene activity that don’t alter DNA itself.

Uncovering the Hidden Chemical Universe

History has provided stark examples of this. For example, children born to mothers who endured famine in the Netherlands during the second world war were more likely to develop heart disease, type 2 diabetes, and schizophrenia later in life. Decades on, scientists found their gene activity had been altered by what their mothers ate – or didn’t eat – while pregnant.

Projects such as the Foodome Project are now attempting to catalogue this hidden chemical universe. More than 130,000 molecules have already been listed, linking food compounds to human proteins, gut microbes, and disease processes.

The aim is to build an atlas of how diet interacts with the body, and to pinpoint which molecules really matter for health. The hope is that by understanding nutritional dark matter, we can answer questions that have long frustrated nutrition science.

Why do certain diets work for some people but not others? Why do foods sometimes prevent, and sometimes promote, disease? Which food molecules could be harnessed to develop new drugs, or new foods?