Low-fiber diets make gut microbes poop out

The high fiber refrain never seems to stop. We all know that we’re supposed to eat more fiber and focus on whole grains, fresh fruits and vegetables. But when forced to choose between chewy, crumbly, flavorless oat bran and delicious white buttered toast for breakfast, it’s easy to tune out. 

But that fiber isn’t for you. It fuels and sustains your gut microbes — and those in your kids, and grandkids and great-grandkids, too, a study in mice finds. The results suggest that when we pass our genes on to our children, we also pass on a gut ecosystem that reflects our previous dietary choices. (No pressure.)

The Food and Drug Administration recommends that Americans eat about 25 grams of dietary fiber per day. But most people don’t hit that mark. “The average American gets 10 to 15 grams of dietary fiber,” says Erica Sonnenburg, a microbiologist at Stanford University.

If that doesn’t make you feel ashamed, compare your diet to the Hadza, hunter-gatherers who live in Tanzania. “The tubers they’re eating are so fibrous [that people] chew for a while and spit it out,” Sonnenburg says. It’s hard to calculate exactly how much fiber the Hadza get from the tubers, but Sonnenburg says that some some speculate it’s between 100 and 150 grams per day at certain times of year.

That high level of fiber is reflected in their guts. “What all the studies have found is that these populations who are living a more traditional lifestyle are the best approximation for our ancient microbiota. They all harbor microbiota that’s much more diverse.”

In the human gut, Sonnenburg says, components of dietary fiber called microbiota-accessible carbohydrates, or MACs, are feasting fare. “These are what the bacteria in our guts thrive on,” she says. The bacteria ferment the carbohydrates, creating fuel, Sonnenburg explains. The chemical products of that fermentation feed the bacteria, but many of them will also get absorbed back into our bodies.

With less fiber in the diet, gut microbes that depend on that fiber might disappear too. But whether that change is permanent, and how this might affect future generations, wasn’t clear. To find out, Sonnenburg and her colleagues created mice that had human gut bacteria. The mice, raised with no natural bacteria of their own, all received a fecal transplant of the same donor human gut bacteria.

The mice were originally raised on a high-fiber diet. Then, half of them were switched to a low-fiber diet, and their gut bugs were tested. After seven weeks, the low-fiber-diet mice were returned to their high-fiber diet. When on the low-fiber diet, animals showed a decrease in the diversity of their microbiome, with 60 percent of the bacteria species plummeting in numbers compared with their high-fiber friends. Going back to a high-fiber diet recovered some of the diversity. But mice that had experienced the low-fiber lifestyle still had 33 percent less microbial diversity than before.

Then, to see if diet affected the mice’s offspring, the scientists bred the mice on low- or high-fiber diets for four generations. They found that pups of mice on the low-fiber diet showed less and less microbial diversity with each generation. By the fourth generation, the mice bred on low-fiber diets had lost 72 percent of the microbial diversity. When the low-fiber–bred pups were switched to a high-fiber diet, there was a small bit of recovery. But the microbial diversity still remained 67 percent lower than that in mice that had always had a high-fiber life. The diversity was restored with another dose of the original human gut bacteria, delivered by fecal transplant.

Of the bacteria lost across generations, 67 percent were Bacteroidales, an order of bacteria that usually dines on fiber in the gut. There was also a drop in a family of proteins called glycoside hydrolases. These bacterial proteins help to degrade carbohydrates, including those from fiber.

“Everyone accepts that we pass our human genes on to our children, but I think now we need to consider that our children also inherit a microbial set of genes from us,” says Sonnenburg. And which microbial genes get passed on will be influenced by our dietary choices.  Sonnenburg and her colleagues published their findings January 13 in Nature.

The study shows that changes to the microbiome aren’t just transient, says Peter Turnbaugh, a microbiologist at the University of California at San Francisco. “The most important thing is showing proof of principle,” he says. “That it’s possible to have a long-lasting effect on the microbiome that translates to future generations. That’s something that hasn’t been seen before.”

While the researchers did the study with human microbes, they were studied in mice. And not very many mice. Only six mice for each generation were examined, and only three animals received the final fecal transplant to restore their gut diversity.

The animals also were living in a sterile environment without other microbes. So they couldn’t have been exposed to any bacteria to make up for the ones they were losing — diversity had nowhere to go but down. So whether the findings would translate to humans is “a good question,” Turnbaugh notes. We received many new microbes as we go about our daily lives. “We may not be intentionally performing microbiome transplants,” Turnbaugh explains. “But we’re being exposed to microbes from our coworkers, the people we live with and the people we pass on the subway.” Those microbes could change the diversity of our guts, even if we only ever eat low-fiber white bread.

“It’s a really neat concept and it’s carried out well,” John Cryan, a neuroscientist at the University College Cork in Ireland, says of the new study. But it’s hard to tell whether the loss of microbiome diversity actually had an effect on the animals’ health. The microbes are definitely missing, and the proteins that digest fiber are missing. But no one knows just what effect that might have on the mice themselves. “I would like to have seen some functional readouts, a consequence of the reduced diversity in these mice.” Maybe the loss changed how much the animals ate, their weight or their behavior.

And whether high-fiber or low-fiber, a lab mouse’s diet is “very undiverse,” Cryan notes. Humans eat many different things over their lifetimes, and many other nutrients, such as proteins or fats, could impact the gut environment as well. Sonnenburg and her colleagues intend to examine similar situations in humans, to see if the effects persist.

Until then, Cryan says, “we have to be careful,” about how much we read into studies like this one. But whether or not our white bread and processed food diets have doomed us and our kids, fiber still remains good for you. “If people realize fiber is good for you in terms of [gut] diversity,” Cryan notes. “I think that’s a good thing.”