Read our COVID-19 research and news.

Gut dweller. Prevotella melaninogenica is one of many bacterial species living in the human intestine whose roles scientists are now exploring.

© Visuals Unlimited/Corbis

Your Gut Bacteria Are What You Eat

What you put into your mouth may help determine what type of bacteria thrive in your gut, according to a new study. Researchers have found that a person's intake of meat, fat, carbohydrates, and alcohol appear to influence the type of bacteria that will set up shop in their intestines—but the study also suggests that dietary changes won't quickly replace one microbial population with another.

Scientists are increasingly interested in the vast, largely unexplored populations of bacteria that live in our guts. Studies suggest that these untold billions of microbes may play a role in diseases such as obesity and inflammatory bowel disease; a recent paper even showed that intestinal bugs can meddle with brain chemistry and behavior in mice. "We're all wrestling with the questions of what bugs are there and what they are doing," says microbiologist Frederic Bushman of the University of Pennsylvania, who led the new study.

A large European-Asian consortium brought some order to the chaos when it reported in a Nature paper in April that humanity can be roughly divided into three "enterotypes" depending on which genus of bacteria dominates in people's gut: Bacteroides, Ruminococcus, or Prevotella. People's enterotype appeared to be stable over time, but it remains unclear why your gut population might be so radically different from your neighbor's.

The new study may provide part of the answer. Bushman and colleagues asked 98 healthy volunteers to fill in two questionnaires, one asking about what they ate and drank recently, the other about their long-term dietary habits. The team also took stool samples from the subjects and analyzed their DNA content to determine the makeup of the gut flora.

In a paper published online today in Science, the team reports a similar clustering into enterotypes—although only two of the three showed up clearly—and discovered that dietary habits are linked to the type of bugs that thrive in the gut. People who eat a lot of meat and saturated fat tended to have more Bacteroides in their flora; Ruminococcus prevailed in people who consumed lots of alcohol and polyunsaturated fats, whereas Prevotella favored a diet rich in carbohydrates. It's not clear whether one type of microbial flora is healthier for the host than the other. But if that turns out to be the case, the study offers hope of new ways to improve health by changing diet, Bushman says.

However, other findings reported in the same paper show that you can't change enterotype overnight. The team sequestered 10 volunteers in a hospital and fed half of them a fixed diet very high in fat and low in fiber; the other half of the subjects had the opposite menu. The researchers found that the bacterial populations began to shift within both groups, with some species becoming more common and others less common, but people had the same enterotype when the study ended after 10 days. If switching gut enterotype is possible, the team concludes, it may take a long-term dietary intervention.

"My gut reaction? It's a very intriguing paper," says Peer Bork, a bio-informatician at the European Molecular Biology Laboratory in Heidelberg, Germany, and a senior author on the April paper in Nature. Bork, who's "very happy" to see the first confirmation of the existence of enterotypes, says little is known so far about the influence of diet on the microbial flora so far but that it may well play a major role. He cautions, however, that the study needs to be repeated with larger numbers of people because there are many potentially confounding factors; for instance, people reporting a lot of meat could also simply eat larger portions or have a different lifestyle that affects their gut flora.

"The study shows nicely that global enterotypes appear stable to short-term dietary interventions," says Alan Shuldiner, who studies the gut microbiome at the University of Maryland School of Medicine in Baltimore. But even the small shifts seen by the team could have an impact on the functioning of the bacterial population and on health, Shuldiner says. The challenge now is to find out how. Also unknown is whether long-term dietary changes have a bigger impact and to what extent people's genes influence their gut flora.

Bushman agrees that the study is just scratching the surface of what is a vast new research program. "We're only beginning to ask the questions we want to answer in the next round," he says.