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The Gut’s Microbiome Changes Rapidly with Diet

A new study finds that populations of bacteria in the gut are highly sensitive to the food we digest



National Institute of Diabetes and Digestive and Kidney Diseases

You are what you eat, and so are the bacteria that live in your gut.

Microbiologists have known for some time that different diets create different gut flora, but previous research has focused on mice instead of humans, leaving the actual relationship between our food and our stomach bacteria unclear. A new study, published Wednesday in Nature, indicates that these changes can happen incredibly fast in the human gut—within three or four days of a big shift in what you eat. “We found that the bacteria that lives in peoples’ guts is surprisingly responsive to change in diet,” Lawrence David, assistant professor at the Duke Institute for Genome Sciences and Policy and one of the study’s authors, says. “Within days we saw not just a variation in the abundance of different kinds of bacteria, but in the kinds of genes they were expressing.” (Scientific American is part of Nature Publishing Group.)

Eugene Chang, a professor of medicine at the University of Chicago who specializes in gastroenterology agrees that the speed is surprising. “One of the major points of this study was that in contrast to what we thought might take days, weeks or years began to happen within hours,” says Chang, who was not part of the study. They also observed changes in the amount of bile acid secreted into the stomach, and found that bacteria native to our food—microorganisms used to produce cheeses and cure meats—are surprisingly resilient, and colonize the gut along with species already in our microbiome.

But why do we care about which critters are helping us digest our food? “The incredible quickness of this shifting is interesting,” David says, “for at least two reasons:” The first is evolutionary. These rapid changes, he says, could have been very useful for ancient humans. For hunters and gatherers, diet could be altered quickly and with little transition—weeks of nuts and seeds might be broken up by a sudden influx of meat from a successful hunt—and the ability to rapidly change the microbiome would ensure maximum nutrient absorption from even the most unfamiliar foods.

For modern humans, the rapid shift could be less adaptive. The 10 participants in the study switched to either a plant- or animal-based diet, with the former avoiding animal products and the latter eating milk, cheese and meat. In the subjects eating animal products the researchers saw a significant uptick in Bilophila wadsworthia, a bacteria known to contribute to colitis, a variety of inflammatory bowel disease, in mice. But the link hasn’t been studied in humans, so David does not think that cheese-lovers are necessarily eating themselves sick. “We’re anticipating that people will try to draw conclusions about which diet is better from this,” David says, “and we want to address that it’s very difficult to come to any health-related judgment based on this study.” Without measurements of host health during the study, like inflammation in the gut or immune system responses, David says, such a connection is impossible to make.

Chang, who has worked on the connection between B. wadsworthia and colitis in mice, agrees that the new study does nothing to prove the same for humans. But he thinks there may be something there. “This study shows how sensitive the body is to dietary change,” he says. “For the lay public, it underscores the importance of diet in health and disease. People should pay more attention to what they eat. But it rests on scientists to recognize that dietary discipline has these varied effects, and to understand what each component does so we can design healthier diets.” Dramatic changes in our diet, he says, could very well be the cause of “Western disorders” such as inflammatory bowel disease and obesity. Still, David says, his study was not meant to change the way we eat.

Follow-up research could monitor host health to support a connection between certain bacteria and disease. Whereas the initial study was small, David says the research team is unlikely to repeat it with a larger group. The results were consistent from one individual to another, so although more participants would add statistical support, he doubts they would see a change in the bacterial activity. “I should also point out,” David says, “that it’s fairly difficult to get even 10 people that will radically change their diet and then track themselves so regularly.” Instead, he anticipates that future studies will explore how things like food preparation change which flora flourish in the gut.

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