What does “dark matter” mean?

In a foundational paper published in Nature Food, researchers compared around 150 routinely tracked nutritional components with more than 26,000 distinct biochemicals identified in food. This was a comparison of the number of components, rather than the proportion of food by weight.

“Dark” refers to gaps in our knowledge. Some compounds have been identified, but their quantities across foods and their contribution to our overall dietary exposure remain poorly mapped. Others are already well studied, yet are rarely included in the tools we use to assess diets.

These compounds are not necessarily harmful, and the term has nothing to do with dark-coloured foods. Equally, being overlooked does not make a compound beneficial or an essential nutrient.

The central idea is simple: a nutrition label provides useful information, while food’s full chemistry extends much further.

A wider world of plant compounds

Polyphenols are one familiar part of this wider picture. This diverse family of plant compounds occurs in foods such as berries, tea, cocoa and olives. Other plant compounds contribute to the colours, aromas and distinctive flavours of everyday ingredients.

These compounds become easier to picture when we look at familiar foods.

Exploring the compounds in everyday foods

Extra virgin olive oil contains hydroxytyrosol, tyrosol, oleocanthal and oleacein. Its phenolic profile varies with the olive variety, growing conditions, production and storage — so two oils can have different compositions despite similar fat content.

Tomatoes contain polyphenols such as naringenin, quercetin and chlorogenic acid. They also provide lycopene, the pigment responsible for much of their red colour. Lycopene is a carotenoid rather than a polyphenol, illustrating how food’s wider chemistry spans several families of compounds.

Broccoli provides flavonols such as kaempferol and quercetin. It also contains glucoraphanin, which can be converted into sulforaphane when the plant tissue is broken up and the appropriate enzyme is active. Sulforaphane belongs to a different chemical family from polyphenols.

Berries offer different mixtures depending on the species. Many contain anthocyanins, including compounds based on cyanidin and delphinidin, which contribute red, blue and purple colours. Raspberries and strawberries also contain ellagitannins, another group of polyphenols. This is one reason to vary your berries rather than always choosing the same type.

Red wine contains resveratrol, catechin, epicatechin and quercetin. Its polyphenols largely originate in grapes, and their amounts vary with grape variety and winemaking. These compounds are part of wine’s chemistry; their presence should not be presented as a reason to drink alcohol.

Green tea and matcha contain catechins, a family of polyphenols that includes epigallocatechin gallate (EGCG), epigallocatechin (EGC), epicatechin gallate (ECG) and epicatechin (EC). With brewed green tea, compounds are extracted into water and the leaves are removed. Matcha is finely powdered green tea, so you consume the leaf itself. The amount of catechins in your cup depends on the tea, the quantity used and how it is prepared.

Coffee provides chlorogenic acids, including caffeoylquinic, feruloylquinic and dicaffeoylquinic acids. These polyphenols add another layer to coffee’s chemistry beyond caffeine. Roasting changes their profile, with lighter roasts generally retaining more chlorogenic acids than darker roasts; the beans and brewing method also influence what ends up in the cup.

These are examples of identified, studied food compounds. They help make food’s chemical richness tangible, while “nutritional dark matter” describes the wider gaps in how that richness is measured and understood.

Some of these substances are being studied for their interactions with cellular signalling, normal metabolic processes and gut microbes. Their effects depend on the compound, the amount consumed and how it is processed by the body.

Even a single food can contain a remarkably complex mixture. A human grape study, for example, highlighted the many phytochemicals present in grapes and explored changes in gut microbes and metabolites during grape consumption. It illustrates why researchers increasingly study whole foods alongside individual compounds: one ingredient delivers many substances together.

This also helps explain why reducing a food to one headline ingredient can miss much of its character.

Your gut helps shape the story

The chemistry of a meal continues to change after we eat it. Digestion releases compounds from food, and gut microbes can transform some of them into smaller molecules called metabolites.

This means that what is present in a food and what eventually becomes available to the body are different parts of the story. People may process the same food differently because of variation in digestion and their microbial communities.

In a small randomised crossover study, researchers observed short-term changes in selected gut bacteria after meals containing a mixture of spices. The findings offer a glimpse of how everyday ingredients can interact with our internal microbial environment; a change in bacteria alone does not establish a health benefit.

Food and the gut form an ongoing biochemical conversation — one that researchers are gradually learning to understand.

Cooking changes food’s chemistry

Preparation matters too. Heating, cooling, drying and fermentation can alter the amount of plant compounds in food and how readily they become available during digestion.

The effects vary. Some processes reduce particular polyphenols, while others help release compounds from the surrounding food structure. The result depends on the ingredient, the method and factors such as cooking time and temperature.

A useful practical approach is to enjoy a mixture of raw and cooked foods, prepared in ways you like. There is no single cooking method that preserves or improves every compound.

Bring more variety to everyday meals

We do not need a complete chemical map of food to make meals more varied and enjoyable. A practical response to this research is to broaden the ingredients we regularly use, alongside meeting familiar needs for protein, fibre, vitamins and minerals.

Start with small additions:

Think of a familiar lunch: adding lentils, parsley, roasted vegetables and an olive oil dressing brings a wider range of ingredients to the plate. The value lies in the overall meal, rather than chasing the highest possible number of food chemicals.

The bigger picture

Nutritional dark matter gives us another reason to stay curious about food. Alongside the nutrients we can count, there is a rich biochemical world still being explored. Everyday variety is a satisfying place to begin.