In a new study using AI and machine learning, researchers from EPFL discovered that both what we eat and how regularly we eat it are key factors influencing gut health.
The gut microbiota is a community of microorganisms, including bacteria, viruses, fungi, and other microbes, that inhabit the digestive system. Some of these microbes support health, while others can be harmful.
Previous research has long shown that diet strongly influences the composition of the gut microbiota. Diets rich in fruits, vegetables, fiber, and nuts are consistently linked to greater microbial diversity and better digestive health.
Now, EPFL researchers have discovered for the first time that how consistently we follow a healthy diet is just as vital for gut health as the quantity or type of food we eat.
The importance of nutritional quality and regularity
In a recent study published in Nature Communications, scientists from EPFL’s Digital Epidemiology Laboratory—part of both the School of Computer and Communication Sciences and the School of Life Sciences—confirmed earlier findings that specific foods, such as fruits and vegetables, promote a more diverse gut microbiota. Collaborating with researchers from the University of California, San Diego, they also uncovered new and notable insights.
Their analysis revealed that maintaining regularity in eating fruits, vegetables, and grains is crucial for developing a healthy gut microbiota. While it has long been assumed that eating nutritious foods consistently is beneficial, supported by messages like “five fruits and vegetables a day,” this study provides concrete evidence for that belief.
“This research clearly shows that you cannot binge on vegetables on your healthy day and then eat in an unhealthy way for the rest of the week or month,” said Associate Professor Marcel Salathé, head of the Digital Epidemiology Lab and co-director of the EPFL AI Center. “In fact, our study suggests that irregular consumption of healthy foods undoes many of their beneficial effects on the gut microbiota. This is a real incentive for future studies to not just look at what people are eating but the patterns of what they are eating over time.”
Predicting diet from the microbiome
Second, the team was also able to show that a person’s gut bacteria and what they eat can predict each other with up to 85% accuracy. With just a simple stool sample — an increasingly common component of medical research — advanced machine learning techniques could predict a person’s diet using their microbiota and vice versa.
“For our collaborators in San Diego, who are some of the world’s leading experts in microbiome research, this was exciting,” explained Salathé. “Getting such data from a stool sample is relatively easy, but understanding someone’s diet is notoriously difficult, it’s data that’s been challenging to collect.”
The power of real-time data
The study was made possible by using detailed nutritional information from about 1000 participants who were part of the “Food & You” cohort.
High-resolution dietary data was collected via the AI-powered app MyFoodRepo, developed by the same EPFL lab, which allowed users to log their meals in real time by snapping photos or scanning barcodes. The app’s AI then analyzed these entries for nutritional content, later verified by human reviewers.
“Historically, nutrition research has relied on food frequency questionnaires and 24-hour dietary recalls. In theory, you could ask somebody to write down everything they eat but in practice, it’s just not done because it’s borderline impossible. Now, the AI is so good that we can do this data collection at a large scale,” said Rohan Singh, a Doctoral Assistant in the Digital Epidemiology Lab and lead author of the paper.
“Our study has been particularly interesting because when you look at lifestyle-oriented gastrointestinal disorders, they often develop gradually. Since nutrition is one of the big contributors to these diseases, analyzes like ours may be able to assess what can be improved in a person’s diet. AI can then help nudge people to adjust their food intake accordingly,” he continued.
Looking ahead
Salathé believes the study’s findings suggest that current dietary guidelines may need to be updated to emphasize not just the types and quantities of food, but the regularity of healthy eating behaviors.
And, while this research project has ended, the MyFoodRepo app continues to be used by the Digital Epidemiology Lab team for other research. They are currently involved in a pilot project on nutrition and cognitive performance, studying potential links between the two.
Also, through the use of barcoded food data from the Food & You study, the researchers are investigating the link between food additives, like emulsifiers, found in ultra-processed foods, and the gut microbiota.
“There’s a strong hypothesis that some of these additives really may negatively impact your microbiota, and we have some early indications that this could indeed be the case. We’re still in the analysis stage, but we are quite excited about early results,” said Salathé.
More generally, they are gratified that the MyFoodRepo app is now opening the door to important nutrition studies globally.
“From the outset, we knew we needed something extremely consumer-friendly and easy to use, while still providing the data that we needed. We built it to serve our own research needs, but also in a way which others would find useful – and it’s now being used in many other nutrition studies globally,” Salathé concluded.
Reference: “Temporal nutrition analysis associates dietary regularity and quality with gut microbiome diversity: insights from the Food & You digital cohort” by Rohan Singh, Daniel McDonald, Alejandra Rios Hernandez, Se Jin Song, Andrew Bartko, Rob Knight and Marcel Salathé, 30 September 2025, Nature Communications.
DOI: 10.1038/s41467-025-63799-z
Funding: The MyFoodRepo app was funded and supported by several organizations, including the Kristian Gerhard Jebsen Foundation, the Seerave Foundation, and the Leenaards Foundation.
Never miss a breakthrough: Join the SciTechDaily newsletter.
Follow us on Google and Google News.
6 Comments
thanks for th
I am a medical anthropologist researcher focusing on cultural causes of disease. Good to see a greater awareness of gut microbiota and its effect on health. However, they need to add the use of tight clothing around the waist, such as belts. Compression of the abdomen with tight clothing may interfere with digestion, circulation of blood and lymph, and impact microbiota dynamics. It’s not just what we put into our bodies that affect our microbiota. What we put outside our bodies also has impacts, especially if it is tight. Anything that leaves marks in the skin is too tight.
Can you cite a study or other evidence to support your claim?
See https://vitagastro.com/why-tight-clothing-around-the-waist-contributes-to-reflux-and-digestive-tension/. There is also virtue in using common sense. Medicine typically ignores the physiological impact of tight clothing, so there are few studies. But this does not diminish the impact.
Why are the scientists going all in on the AI, when the key issues with it, such as hallucinations, haven’t been resolved, and perhaps will never be?
Why should I, as an interested party, trust any research that’s been “AI driven”?
“… specific foods, such as fruits and vegetables, promote a more diverse gut microbiota.”
The implication is that a diverse gut microbiota is desirable. Consider that, if one’s diet is diverse, then there is a NEED for diversity to maximally take advantage of the different kinds of potentially digestible foods. That is, if one’s diet consists of corn, beans, squash, and an occasional rabbit, there is no need for a diversity in gut biota; diversity may be a liability with a restricted diet because the gut biota are not optimized for that diet. I have read that American prisoners of war in Vietnam, used to diverse and high-protein diets, took awhile to start using rice effectively as their main food source.