A large new study suggests that stool samples may offer a surprisingly detailed picture of what we eat and how our gut microbes break down those foods. The findings, published in Nature Communications, show that the mix of molecules in stool, known as the fecal metabolome, can reflect dietary patterns and provide clues about gut microbial activity that may relate to future health.
Researchers at King’s College London analyzed data from 2,647 adults in two major UK cohorts, combining stool metabolite profiles with information on gut microbe species and detailed food questionnaires. They examined 650 metabolites produced during digestion, many of which form when gut microbes interact with the foods we eat.
Robert Pope, lead author and PhD student, said the team wanted a clearer way to connect diet with the microbiome.
“Measuring diet and how the gut microbiome responds to different foods is challenging,” he said. He noted that stool metabolites offer a more objective measure than food logs. “Analyzing compounds in stool provides insights into what people eat and how the gut microbiome metabolizes food differently.”
Using machine learning, the researchers found that stool metabolites reflected intake across 10 food and beverage groups, including whole grains, nuts, meat and tea and coffee. They also tracked how these metabolites aligned with overall healthy or unhealthy eating patterns. More than 400 links emerged between specific foods and stool metabolites, with over half showing that higher consumption of certain foods led to higher levels of certain metabolites. The team also identified more than 2,500 relationships between gut microbe species and diet-related metabolites, suggesting that microbial activity plays a major role in shaping the chemical profile of stool.
Because the DASH dietary pattern has well-established heart health benefits, the researchers explored whether stool metabolites could help identify people at higher or lower cardiovascular risk. Models using only DASH score and BMI had moderate accuracy. When researchers used stool metabolites and BMI instead, the models performed better at distinguishing individuals with higher or lower predicted 10-year cardiovascular disease risk. The authors note that this does not mean stool tests can diagnose heart disease, but the findings show potential for new tools that reflect how diet and microbial activity relate to long-term health.
Dr Mario Falchi, co-senior author, said the work highlights how food-derived molecules may support beneficial microbial activity.
“By analyzing 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,” he said.
He explained that this may guide the development of prebiotics that support gut and overall health.
The team also found that a smaller set of 54 metabolites was still effective at identifying dietary patterns, which could lead to simpler and more accessible testing methods in future nutrition research.
Dr Cristina Menni, co-senior author, said the results reveal how diet and gut microbes interact in daily life.
“These findings bring us closer to turning simple stool analyses into powerful tools for understanding how diet and gut microbes interact,” she said.
She noted that the goal is to inform dietary strategies that support health “from the inside out.”
The researchers say fecal metabolomics could help clarify how specific foods influence gut microbial activity and may one day support personalized dietary approaches, though more work is needed before stool-based assessments enter clinical practice.
This research was funded by the Chronic Disease Research Foundation.