Scientists have studied the relationship of nutrition and physical activity with the gut microbiome

Coffee, vegetables, and physical activity are associated with certain features of the intestinal microbiota, while prolonged sitting and an excess of refined carbohydrates are associated with other bacterial profiles. This conclusion was reached by researchers who studied the data of almost 6.8 thousand people and compared the composition of intestinal bacteria with daily habits and health status. About what patterns scientists have discovered and why they do not yet prove the direct influence of lifestyle on the development of diseases — in the material "Izvestia".

How scientists have studied the relationship between the microbiome and lifestyle

The study is published in the journal Nature Medicine. The researchers analyzed data from 6,803 Japanese project participants aged 16 to 95 years. They studied the composition of the intestinal microbiota and compared it with 28 lifestyle factors, including eating habits, physical activity, smoking and time spent in a sitting position.

In addition, the researchers assessed the links between microbiome features, general health, and 15 chronic diseases. These include inflammatory bowel diseases, irritable bowel syndrome, type 2 diabetes, cardiovascular and respiratory disorders. For some of the participants, the scientists also measured the content of short-chain fatty acids in the intestine and indicators of inflammation in the blood.

The task was not only to find the bacteria found in people with certain habits. The authors tried to find out whether the features of the microbiome could statistically explain some of the links between lifestyle and health status. To do this, they used an analysis of intermediary mechanisms: it allows us to assess what role certain microorganisms may play in the discovered relationships, but does not establish causality by itself.

Coffee, vegetables and movement: which bacteria have been linked to lifestyle

Plant-based foods, coffee, fermented foods, and physical activity were predominantly associated with microbial profiles, which the researchers attributed to being associated with better health outcomes. In particular, vegetables, fruits, and mushrooms were correlated with microorganisms involved in the breakdown of plant dietary fibers and other complex carbohydrates such as pectin, hemicellulose, and cellulose.

Among the bacteria associated with such profiles, scientists have identified several species capable of producing butyrate, a short—chain fatty acid formed as a result of the work of the intestinal microbiota. This group includes Faecalibacterium prausnitzii, Anaerostipes hadrus, and Fusicatenibacter saccharivorans. Such microbial features were more common in people with more favorable health indicators.

The researchers paid special attention to coffee. Its use turned out to be associated with microbiome profiles, which also included butyrate—producing bacteria. Lawsonibacter asaccharolyticus has become a potential mediator between coffee consumption and a lower likelihood of inflammatory bowel disease. However, this pattern reflects a statistical relationship rather than a proven protective effect of the drink.

Physical activity was also correlated with the presence of butyrate-producing bacteria. At the same time, the scientists found that the microbial features attributed to the favorable group were generally associated with a higher content of short-chain fatty acids and lower levels of certain inflammatory markers. This suggests that the microbiome may be one of the links linking daily habits with the state of the body.

Scientists talked about the effects of coffee on the intestines and brain

Sedentary lifestyle and refined carbohydrates

The researchers saw a different picture when analyzing prolonged sitting and consumption of refined carbohydrates. These factors were mainly correlated with microbial profiles, which the authors associated with chronic diseases. In particular, prolonged sitting was associated with the presence of species such as Escherichia coli and Ruminococcus gnavus.

The consumption of refined carbohydrates—including rice, bread, noodles, and sugary carbonated drinks—was associated with other features of the microbiota. Among the related microorganisms, the researchers found bacteria of the genus Streptococcus, as well as Klebsiella pneumoniae, Escherichia coli and Morganella morganii. Some of the identified microbial functions were associated with starch and sugar processing, lactate formation, and biofilm formation.

The authors also found that among the microorganisms associated with unfavorable health indicators, bacteria that usually live in the oral cavity and microorganisms that can, under certain conditions, participate in the development of diseases were more common. No such bacteria were found in the group of microbial features associated with more favorable indicators.

The study took into account other habits, including alcohol consumption, but the authors found the main patterns specifically for plant-based foods, coffee, physical activity, prolonged sitting, and refined carbohydrates.

Scientists have named the acceptable time for long sitting

Is it possible to assess health by the composition of intestinal bacteria

Based on the data obtained, scientists have developed a MADE—model system that uses information about the composition of the intestinal microbiota to distinguish between people with and without certain diseases. The researchers tested it on data from a Japanese group, and then evaluated the work on 13 independent samples from different countries. Similar patterns were confirmed in 11 of them, but the accuracy of the model varied depending on the disease. For example, for irritable bowel syndrome, the ability to distinguish between groups turned out to be limited.

Adding age, gender, body mass index, and lifestyle information to the microbiome data improved prediction for some of the conditions studied. Nevertheless, the authors do not yet consider such a system to be a ready-made diagnostic tool: its clinical applicability and practical value of microbiome testing require further verification.

The study has other limitations. The participants reported data on nutrition and some habits on their own, so inaccuracies and the influence of unaccounted-for factors cannot be completely excluded. In addition, the main sample consisted of Japanese residents, and the results have yet to be tested on broader populations.

Finally, the identified links do not prove that specific foods or physical activity directly change the composition of the microbiome and thus prevent diseases. The researchers tested possible intermediary mechanisms, including the reverse direction of the connections, but this does not allow to establish a cause-and-effect relationship. This will require experimental work and clinical studies in which scientists will be able to trace how purposeful habit change affects the microbiota and human health.