Stool chemistry may reveal your diet, and signal heart risk

A simple stool sample may hold a clearer record of what you eat than a food diary ever could.

In a new study, researchers analyzed the “faecal metabolome,” the mix of small molecules in stool created as your gut and its microbes break down food. Those chemical traces captured the push and pull between diet and the gut microbiome, and they helped predict both eating patterns and future heart disease risk.

The team studied 2,647 adults from two large U.K. cohorts, TwinsUK and ZOE PREDICT1. They combined three kinds of information: detailed diet questionnaires, gut microbe species data, and measurements of 650 stool metabolites. Then they used machine learning to test what those metabolites could reveal about everyday eating habits.

The results suggest stool chemistry can act like a “receipt” from your gut. It reflects what goes in, and what your microbes do with it.

Diet plays a major role in health and disease. Gut microbes also link to disease risk, and they change how they behave when your diet changes. When microbes respond to food, they create different metabolites. Those metabolites end up in stool.

That idea sounds simple. Measuring it is not.

Food surveys rely on memory and honesty. Even careful people forget snacks, portion sizes, and habits. Stool metabolites offer a different path. They capture the outcome of digestion and microbial processing, not just what you meant to eat.

Robert Pope, a PhD student at King’s College London and lead author, said: “Measuring diet and how the gut microbiome responds to different foods is challenging. Analyzing compounds in stool provides insights into what people eat and how the gut microbiome metabolizes food differently, highlighting its role in health.”

The researchers found stool metabolites reflected intake of 10 food and beverage groups. These included meat, nuts, wholegrains, and tea and coffee. The metabolite patterns also tracked whether someone followed healthier or less healthy eating styles overall.

The study identified more than 400 links between specific food groups and metabolites. More than half were positive. That means higher intake of a food group matched higher levels of certain metabolites.

Those metabolites likely come from two sources. Some may be in foods directly. Others may form when microbes break foods down.

"Our team also mapped how microbes fit into the picture. We found more than 2,500 connections between gut microbial species and over 90% of the diet-linked metabolites. About one quarter of these diet-related metabolites also tracked with overall gut microbial diversity," Pope shared with The Brighter Side of News.

That matters because diversity often reflects how rich and varied the gut ecosystem is. The study did not claim diversity alone determines health. Still, it showed diet-linked stool chemistry can line up with broader microbial patterns.

Among the dietary measures tested, stool metabolites performed best at tracking the DASH diet, short for Dietary Approaches to Stop Hypertension. DASH is widely known for benefits tied to heart health.

That raised a bigger question. If stool metabolites can reflect DASH adherence, could they also help predict future cardiovascular risk?

The researchers tested models for 10-year cardiovascular disease risk. Models using only the DASH score and body mass index showed moderate accuracy. But models using faecal metabolites and body mass index performed better. They more accurately separated people at higher risk from those at lower risk.

In other words, stool chemistry captured something diet scores missed. It may reflect not only what you eat, but how your body and microbes process it.

Dr Mario Falchi, Reader in Computational Medicine at King’s College London and co-senior author, said: “By analysing the chemical fingerprints left by our diet in the gut, we can identify which food-derived molecules nourish the microbiome and promote their production of beneficial compounds; guiding the development of prebiotics that support both gut and overall health, regardless of diet or food access.”

Measuring 650 metabolites can be costly and complex. The team tested whether a smaller set could still work.

They found a subset of 54 metabolites still predicted dietary patterns and food group intake well. That smaller panel could support simpler testing methods in future nutrition and clinical research.

Dr Cristina Menni, co-senior author and Senior Lecturer in Molecular Epidemiology at King’s College London, said: “These findings bring us closer to turning simple stool analyses into powerful tools for understanding how diet and gut microbes interact; helping to design dietary strategies that improve health from the inside out.”

The work points to a future where nutrition studies rely less on self-report. It also suggests new ways to identify food-microbe combinations that support better health.

This study suggests stool metabolite profiles could become practical tools for nutrition science. They may provide more objective measures of diet than questionnaires alone. That can strengthen research on how eating habits affect disease risk.

The findings also hint at new paths for personalized nutrition. If stool metabolites show how your microbes handle foods, future diets could be tailored to your gut response, not just general advice.

The research may also guide development of prebiotics. By identifying which food-derived molecules support helpful microbial activity, scientists can design targeted compounds that promote beneficial metabolite production.

Finally, the smaller 54-metabolite panel raises the possibility of simpler, more accessible testing. That could help both research studies and clinical screening, if validated further.

Research findings are available online in the journal Nature Communications.

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