Diet influences the composition and function of the gut microbiota, and in turn, these microorganisms can modify the health-promoting properties of food, helping to explain why people react differently to the same foods. Although a tomato is a tomato, it doesn’t benefit everyone in the same way. So, why shall we continue recommending it for everyone?
This question is at the heart of a recent review co-authored by Yolanda Sanz, full professor of the Spanish Research Council (CSIC) at the Institute of Agrochemistry and Food Technology (IATA), and Patrick Veiga, research director at the MICALIS Institute and MetaGenoPolis at INRAE, published in Nature Reviews Gastroenterology & Hepatology. In it, they highlight how microbiota research paves the way for precision nutrition, a step forward from one-size-fits-all dietary guidelines.
In this review, you explore the link between diet and microbiome —a two-way street — and you reinforce a concept that has been in the field for some years already: there is not a one-size-fits-all diet.
SANZ: What makes this review special is that we’re not just talking about [gut microbiome-diet] associations anymore. We’re moving toward mechanisms and causality—and importantly, toward translating science into practical tools to improve public health.
Are current dietary guidelines valid?
SANZ: Up until now, those guidelines and recommendations for healthy diets, based on the intake of specific foods established by competent national bodies in each country, have not considered what research on the microbiome contributes.
In the article, you highlight the case of fiber and the universal recommendation of 20 to 35 grams per day for adults.
VEIGA: Fiber recommendations are still based on bowel movement data from decades ago. The standard 25 grams per day was established when we thought only about digestion and local effects on the intestine. Today, we suspect that more than the recommended intakes might be needed to better prevent chronic diseases— but we don’t yet have enough data to confirm it, especially because most people only eat 20 grams per day. So, we can’t yet establish how much fiber would be optimal to protect you from non-communicable diseases — such as cardiovascular diseases, diabetes, chronic respiratory diseases, and cancer— and to what extent fiber type matters.
SANZ: Fiber is an umbrella term for a diverse group of substances that cannot be digested in the small intestine. Different types (of fiber) behave differently, and not everyone benefits the same. For people with inflammatory conditions like Crohn’s, some fibers can help, while others might worsen symptoms. This nuance is not reflected in current general recommendations intended for general healthy population.
Does the same apply to fermented foods?
VEIGA: We know being exposed to non-pathogenic germs and microbes stimulate your immune system, but we don’t yet have the data in different groups of people to confirm and define how much live non-pathogenic microbes — the ones included in fermented foods, for example — you should consume every day, or how this may vary across populations. We also have evidence that people’s microbiome responds differently to fermented foods — some being permissive, others being resistant. So that’s why we can’t give the same recommendation for the whole population, and we really need to stratify people -based on factors such as gender, age, socioeconomic status and diet, among others-. In the paper, we advocate for stratified precision nutrition, which is not personalized nutrition.
What’s the difference?
VEIGA: Personalized nutrition targets the individual, which is very strong and relevant for the medical field because it can save lives, but it is not scalable to entire populations. Precision nutrition, instead, means creating subgroups based on factors like microbiota composition to deliver better dietary advice at a public health level.
Do we have enough scientific knowledge to do it?
VEIGA: In the near future there are some studies that will help us to bridge this gap. For instance, The French Gut project that we launched in France will collect microbiome and dietary data from 100,000 people and will follow the health of the population over 20 years, with the aim to identify biomarkers that can predict who benefits from what. Hopefully, we will be able to understand why some subgroups of people are more protected against diseases compared to others and whether their microbiome is playing a role in that. We aim at identifying measurable indicators or signs that reflect what is taking place in the body (biomarkers) that will help us to distinguish these subgroups that might be at risk and might benefit from precision nutrition recommendations.
SANZ: Also, we need to study more how diet affects sick versus healthy individuals. That’s largely missing and could help guide nutrition for people with chronic conditions.”
Can you give us a real-world example?
SANZ: Take polyphenols, which are naturally occurring compounds found in plant foods, such as fruits, vegetables, herbs, spices, tea, and dark chocolate: they are considered beneficial for health, but their effects depend on how your gut microbiota transforms them. Therefore, two individuals, even healthy, may react very differently to the same polyphenol.
VEIGA: We’re just beginning to uncover how the microbiota shapes the health effects of dietary components, for better or worse. It’s time our diet recommendations reflect this complexity.
Time matters too. Our gut bacteria like regularity.
VEIGA: As your genes, your gut bacteria have a biological clock too. So, if you have lunch daily at noon, both your genes and microbiota prepare for it. Eating regularly really matters.
How do you imagine the doctor’s visit in the future?
VEIGA AND SANZ: In the future, your doctor might analyze your microbiota the same way they check on your cholesterol. And if, for instance, your microbiota produces certain metabolites linked to cardiovascular risk, such as TMAO, they could say: “Look, you have a bit of cardiovascular risk because your cholesterol is high, but on top of that, you have TMA-related metabolites—so try to avoid these and those specific foods that are used by those bacteria increasing your disease risk. This is where we’re headed—using the microbiota to guide dietary decisions more precisely.
This interview has been edited for length and clarity.
Reference:
Sanz Y, Cryan JF, Deschasaux-Tanguy M, et al. The gut microbiome connects nutrition and human health. Nat Rev Gastroenterol Hepatol. 2025; 22(8):534-555. doi: 10.1038/s41575-025-01077-5.
