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BACK IN 2003, the Human Genome Project promised to unlock the secrets of health and disease. Instead, it revealed something startling: our genes explain barely ten per cent of the risks we face. The rest? It’s down to the environment — and what we eat looms large.
The catch: we’ve only been looking at food through a keyhole. Nutrition advice has typically meant counting fats, sugars, or proteins. In reality, scientists estimate our diet delivers over 26,000 compounds. Only around 150 are well understood. The rest are invisible to us, but not to our bodies.
Astronomers call the unseen stuff holding galaxies together dark matter. Nutritionists are now talking about nutritional dark matter — the chemical universe in our food that we barely comprehend.
FOOD AS CHEMISTRY, NOT JUST CALORIES
Take the Mediterranean diet. We know it lowers heart disease risk. But why? It’s not just the olive oil or the fish. It’s also in the quiet chemistry.
When you eat red meat or eggs, gut bacteria produce a compound called TMAO (trimethylamine N-oxide), which raises heart disease risk. Garlic, however, contains natural blockers that stop TMAO forming. In other words, your plate is staging a chemical drama every time you sit down to lunch.
Nutrition science is moving beyond the simplistic idea of food as “fuel” and towards foodomics — the study of how diet interacts with genes, proteins, metabolism and microbes.
THE ALCHEMISTS IN YOUR GUT
Much of this hidden chemistry happens thanks to your gut bacteria. When compounds travel to the colon, microbes remix them into new molecules with surprising effects.
Example: ellagic acid, found in fruits and nuts, is transformed by gut microbes into urolithins, which help keep mitochondria (your cells’ power plants) healthy.
That means a handful of walnuts or pomegranate seeds isn’t just a snack. It’s a biochemical starter kit waiting for your microbes to work their magic.
FOOD CAN SWITCH YOUR GENES ON OR OFF
It’s not just what you eat today. Food can influence gene activity for decades. During the Dutch famine circa World War II, mothers who endured hunger gave birth to children more prone to heart disease, diabetes and even schizophrenia later in life. The lack of nutrition had effectively “switched” certain genes on or off without altering DNA itself — a field known as epigenetics.
Which means your dinner isn’t just fuelling your body. It could be rewriting its rulebook.
Enter: The Foodome Project, a global effort to catalogue the hidden molecules in our meals. Already, more than 130,000 compounds have been listed, with links to human proteins, gut microbes and diseases. The ambition is huge: an atlas showing how food interacts with the body, molecule by molecule.
It’s a bit like mapping the stars — slow, meticulous, but ultimately revolutionary.
WHY THIS MATTERS TO YOU
Here’s the kicker: not all nutritional dark matter is good. Some compounds may promote health, others might quietly raise your risk of disease. Understanding them could explain why diets work for some people and flop for others. It could even inspire new drugs or designer foods based on these hidden molecules.
For now, the practical lesson isn’t to obsess over every unknown compound — we don’t yet know what most of them do. Instead, the takeaway is that a diverse diet, rich in fruits, vegetables, whole grains, legumes, nuts and spices, gives your body (and your microbes) the widest set of building blocks to work with.
Just as astronomers chart galaxies through dark matter, nutritionists are slowly sketching the outlines of our hidden food universe. And while the full map isn’t drawn yet, one thing is certain: every bite contains more than meets the eye — or the label.
This article is adapted from a paper titled "What Exactly Are You Eating? The Nutritional ‘Dark Matter’ In Your Food", authored by David Benton, and originally published on The Conversation.
