Scientists know that the trillions of bacteria and other microbes that live in our intestines play an important role in health, influencing our risk of developing obesity, heart disease, type 2 diabetes and a wide range of other conditions. But now a major new international study has found that the composition of these microorganisms, collectively known as our microbiomes, is largely shaped by what we eat.
In analyzing the diets, health and microbiomes of more than 1,000 people, the researchers found that a diet rich in whole foods and dense in nutrients supported the growth of beneficial microbes that promoted good health. But eating a diet full of highly processed foods with added sugars, salt and other additives had the opposite effect, promoting intestinal microbes that were linked to poorer cardiovascular and metabolic health.
The researchers found that what people ate had a more powerful impact on the composition of their microbiomes than their genes. They also found that a variety of plant and animal foods were linked to a more favorable microbiome.
A critical factor was whether people ate highly processed foods or not. People who tended to eat minimally processed foods, such as vegetables, nuts, eggs and seafood, were more likely to harbor beneficial intestinal bacteria. Consuming large quantities of juices, sweetened drinks, white bread, refined grains and processed meats, on the other hand, was associated with microbes linked to poor metabolic health.
“This goes back to the old message of eating as much whole and unprocessed food as possible,” said Dr. Sarah E. Berry, nutrition scientist at King’s College London and co-author of the new study, which was published Monday in Nature Medicine. “What this research shows for the first time is the link between the quality of the food we eat, the quality of our microbiomes and, ultimately, our health outcomes.”
The findings may one day help doctors and nutritionists to prevent or perhaps even treat some diet-related illnesses, allowing them to prescribe personalized diets for people based on the unique composition of their microbiomes and other factors.
Many studies suggest that there is no standard diet that works for everyone. The new study, for example, found that while some foods are generally better for health than others, different people may have entirely different metabolic responses to the same foods, mediated in part by the types of microbes that reside in their intestines.
“What we found in our study was that the same diet in two different individuals does not lead to the same microbiome and does not lead to the same metabolic response,” said Dr. Andrew T. Chan, co-author of the study and professor of medicine at Harvard Medical School and Massachusetts General Hospital. “There is a lot of variation.”
The new findings are the result of an international study of personalized nutrition called Predict, which is the world’s largest research project designed to look at individual responses to food. Started in 2018 by British epidemiologist Tim Spector, the study followed more than 1,100, mostly healthy adults, in the United States and Britain, including hundreds of identical and non-identical twins.
The researchers collected data on a wide range of factors that influence metabolism and disease risk. They analyzed the participants’ diets, microbiomes and body fat. They took blood samples before and after meals to check blood sugar levels, hormones, cholesterol and inflammation. They monitored their sleep and physical activity. And for two weeks they used continuous glucose monitors that monitored their blood sugar responses to different meals.
The researchers were surprised to find that genetics played only a minor role in the formation of a person’s microbiome. Identical twins were found to share only 34% of the same intestinal microbes, while unrelated people share about 30% of the same microbes. The composition of each person’s microbiome seemed, instead, to be driven more by what they ate, and the types of microbes in their intestines played an important role in their metabolic health.
The researchers identified groups of so-called good intestinal insects, which were more common in people who ate a diverse diet rich in high-fiber plants – such as spinach, broccoli, tomatoes, nuts and seeds – as well as minimally processed animal foods, such as fish and whole yogurt. They also found groups of “bad” insects in the gut that were common in people who regularly consumed highly processed foods. A common denominator among highly processed foods is that they tend to contain very little fiber, a macronutrient that helps nourish good microbes in the gut, the researchers said.
Among the “good” strains of intestinal microbes were Prevotella copri and Blastocystis, both associated with lower levels of visceral fat, the type that accumulates around internal organs and increases the risk of heart disease. These microbes also appear to improve blood sugar control, an indicator of diabetes risk. Other beneficial microbes have been linked to reduced inflammation and reduced spikes in blood fat and cholesterol levels after meals, all playing a role in cardiovascular health.
The new study was funded and supported by Zoe Global, a health sciences company, as well as the Wellcome Trust, a British nonprofit, and several public health groups.
Dr. Berry said the findings suggest that, by looking at the profiles of the microbiome, they can identify people at high risk of developing metabolic diseases and intervene early. She and her colleagues are now planning a clinical trial that will test whether telling people to change specific foods in their diets can alter the levels of good and bad microbes in their intestines and subsequently improve their health.
“We think there are many small changes that people can make that can have a big impact on their health, which can be mediated by the microbiome,” she said.