The Modern Low-Fiber Diet May Be Damaging Our Microbiomes

We don’t talk about fiber all that much anymore. The high-fiber diet craze of the 1980s died quietly beneath the heel of the 1990s fat-free foods juggernaut, leaving lonely bran muffins to go stale in pastry cases. But fiber, passé though it may be, is still incredibly important for our health. A new study suggests that eating low-fiber processed food can weaken our microbiomes—and that we pass that weakness on to our descendants. The researchers published their findings today in the journal Nature.

This is a bigger deal than you might think. The communities of microorganisms that make up your microbiome affect more than just your gut. Researchers have linked microbiome health with depression, overeating, sexually transmitted disease, and more. It’s in our best interest to keep the tiny ecosystems in our bodies happy and healthy.

The first bacterial deposit in your microbiome bank was made while you were still in the womb. People take in bacteria through the birth canal, through breast milk, and through contact with their mothers’ skin. So the health of your family members’ microbiomes has a big impact on your own. And if their little ecosystems were deficient in some way, they could pass that deficiency on to you.

And unfortunately, we are looking a little deficient these days, says Stanford University microbiologist Erica D. Sonnenburg, the study’s lead author. “Numerous factors including widespread antibiotic use, more-frequent cesarean sections and less-frequent breastfeeding have been proposed for why we see this depletion in industrialized populations," Sonnenburg said in a press release. “We asked ourselves whether the huge difference in dietary fiber intake between traditional and modern populations could, alone, account for it.”

Why fiber? Fiber is hard for us to digest, so it passes through the intestines without being fully broken down. When those fiber leftovers reach the colon, they become a feast for the bacteria that live there. We need to keep feeding those bacteria to keep them alive. If they don’t get enough fiber, they’re not going to make it.

The odds are that our colon bacteria aren’t getting enough fiber. Our modern diets rely pretty heavily on processed foods, including white flour—that is, flour from which the fiber-rich husk has already been removed. Erica Sonnenburg’s husband Justin works with her at Stanford and was senior author of the study. He notes that members of industrialized societies are only getting about 15 grams of fiber a day. That’s one-tenth the amount consumed by hunter-gatherers, whose microbiomes are said to most closely resemble those of early humans.

So the Sonnenburgs and their colleagues set out to learn how a low-fiber diet affects the microbiome. They were curious about the changes both in individuals and across generations.

The researchers fed high-fiber and low-fiber foods to laboratory mice that had been specially bred for this purpose. The mice had been raised in sterile environments, which meant that they were starting with blank microbial slates. First, the mice were given a dose of bacteria taken from a human gut in order to reproduce the conditions of a human microbiome. Then the mice were divided into two groups. The first group ate a diet that contained plenty of plant-based fiber. The second group ate an identical diet, with one difference: Theirs contained almost no fiber.

The mouse poop was collected and tested at the beginning of the experiment and several weeks later. On day one, all of the mouse microbiomes looked pretty much the same. But a clear difference emerged pretty quickly.

“Within a couple of weeks, we saw a massive change," Justin Sonnenburg said in the press release. "The low-fiber-intake mice harbored fewer bacterial species in their gut." And not just a few less; some of the mice had lost more than 75 percent of the species they’d harbored at the beginning.

In the seventh week, the low-fiber mice were switched to high-fiber chow. After four weeks on this diet, the mice’s microbiomes had partially recovered—but only partially.

In a second experiment, the researchers bred several generations of mice, feeding them all a low-fiber diet. The mouse microbiomes became less and less diverse with every new generation. By the fourth round, the mice hosted only 25 percent of the bacterial species found in their great-grandparents. As before, changing the mice to a high-fiber diet helped some, but many of the species were irretrievably gone.

One thing did work: poop transplants. When the researchers implanted fecal bacteria from high-fiber-eating mice into their low-fiber counterparts, the microbiomes of the low-fiber mice made a full recovery.

So what does this mean for humans? “The extremely low-fiber intake in industrialized countries has occurred relatively recently," Justin Sonnenburg said in the press release. "Is it possible that over the next few generations we'll lose even more species in our gut? And what will the ramifications be for our health?"

We don't know yet. But in the meantime, it might not be a bad idea to give that bran muffin another try. Think of your grandchildren.