KEYSTONE, Colo.—Your gut is the site of constant turf wars. Hundreds of bacterial species—along with fungi, archaea and viruses—do battle daily, competing for resources. Some companies advocate for consuming more probiotics, live beneficial bacteria, to improve microbial communities in our gut, but more and more research supports the idea that the most powerful approach might be to better feed the good bacteria we already harbor. Their meal of choice? Fiber.  
Fiber has long been linked to better health, but new research shows how the gut microbiota might play a role in this pattern. One investigation discovered that adding more fiber to the diet can trigger a shift from a microbial profile linked to obesity to one correlated with a leaner physique. Another recent study shows that when microbes are starved of fiber, they can start to feed on the protective mucus lining of the gut, possibly triggering inflammation and disease.
"Diet is one of the most powerful tools we have for changing the microbiota," Justin Sonnenburg, a biologist at Stanford University, said earlier this month at a Keystone Symposia conference on the gut microbiome. "Dietary fiber and diversity of the microbiota complement each other for better health outcomes." In particular, beneficial microbes feast on fermentable fibers—which can come from various vegetables, whole grains and other foods—that resist digestion by human-made enzymes as they travel down the digestive tract. These fibers arrive in the large intestine relatively intact, ready to be devoured by our microbial multitudes. Microbes can extract the fiber's extra energy, nutrients, vitamins and other compounds for us. Short-chain fatty acids obtained from fiber are of particular interest, as they have been linked to improved immune function, decreased inflammation and protection against obesity.
Today's Western diet, however, is exceedingly fiber-poor by historical standards. It contains roughly 15 grams of fiber daily, Sonnenburg noted. For most of our early history as hunter-gatherers, we were likely eating close to 10 times that amount of fiber each day. "Imagine the effect that has on our microbiota over the course of our evolution," he said.
Your bugs are what you eat
Not all helpful fiber, however, needs to come from the roots and roughage for which our ancestors foraged, new research suggests. Kelly Swanson, a professor of comparative nutrition at the University of Illinois at Urbana-Champaign, and his team found that simply adding a fiber-enriched snack bar to subjects' daily diets could swing microbial profiles in a matter of weeks. In a small study of 21 healthy adults with average U.S. fiber intake, one daily fiber snack bar (containing 21 grams of fiber) for three weeks significantly increased the number of Bacteroidetes bacteria and decreased the number of Firmicutes compared with levels before the study or after three weeks of eating fiber-free bars. Such a ratio—of more Bacteroidetes to fewer Firmicutes—is correlated with lower BMI. The findings were published in the January issue of the American Journal of Clinical Nutrition.
"We've known forever that if you eat a lot of fiber, you lose weight," Swanson says. His and other recent studies suggest that our gut microbes are a key player in this relationship. In addition to identifying groups of bacteria, a genome scan revealed a shifting pattern of genes active in the gut microbes. As fiber consumption increased, the activity of genes associated with protein metabolism declined, a finding that researchers hope will help them understand the complicated puzzle of diet and weight loss. "We're getting closer to what is actually cause and effect," Swanson says. 
Feed the microbes so they don't feed on you
As gut microbes are starved of fermentable fiber, some do die off. Others, however, are able to switch to another food source in the gut: the mucus lining that helps keep the gut wall intact and free from infection.
In a recent study presented at the Keystone meeting, Eric Martens of the University of Michigan Medical School, postdoctoral researcher Mahesh Desai and their colleagues found that this fuel switch had striking consequences in rodents. A group of mice fed a high-fiber diet had healthy gut lining, but for mice on a fiber-free diet, "the mucus layer becomes dramatically diminished," he explained at the meeting. This shift might sometimes have severe health consequences. Research by a Swedish team, published last year in the journal Gut, showed a link between bacteria penetrating the mucus layer and ulcerative colitis, a painful chronic bowel disease.
A third group of mice received high-fiber chow and fiber-free chow on alternating days—"like what we would do if we were being bad and eating McDonald's one day and eating our whole grains the next," Martens joked. Even the part-time high-fiber diet was not enough to keep guts healthy: these mice had a mucus layer about half the thickness of mice on the consistently high-fiber diet. If we can extend these results to humans, he said, it "tells us that even eating your whole fiber foods every other day is still not enough to protect you. You need to eat a high-fiber diet every day to keep a healthy gut." Along the same lines, Swanson's group found that the gut microbiomes of his adult subjects reverted back to initial profiles as soon as the high-fiber bars were discontinued.
Martens and his colleagues also observed that mice on the consistently high-fiber diet consumed fewer calories and were slimmer than those on the fiber-free diet, showing that fiber benefits the body in multiple ways. "Studies like this are great because it's getting at the mechanisms to explain why fiber is beneficial," Swanson says.
As all this work underscores, the gut microbiome is exceptionally plastic. Such rapid, diet-influenced changes likely served us well over the course of our evolutionary history—shifting faster than our own physiology could, wrote Justin Sonnenburg and Erica Sonnenburg in a November 2014 article in Cell Metabolism. "In delegating part of our digestion and calorie harvest to our gut residents, the microbial part of our biology could easily adjust to day-to-day or season-to-season variation in available food," they noted. New studies continue to demonstrate that microbial changes due to diet are "largely reversible on short time scales." But the question remains as to how chronic low-fiber intake—over a lifetime or generations—might permanently alter our guts and our health.

The gut microbiota plays a crucial role in maintaining our body's overall health. New research shows what happens if we do not feed our gut microbes with the fiber they need to survive.
[intestinal bacteria under a magnifying glass]
Gut bacteria are essential to keeping our body healthy.
Our gut microbiota contains at least 1,000 different species of known bacteria, summing up 3 million genes.
We share one third of our gut bacteria with other people, while the composition in our other two thirds is unique to each one of us.
Gut microbiota is important to our health because it contributes to a healthy immune system by acting as a barrier against other harmful microorganisms
It also helps with digesting foods that the stomach and small intestine have not been able to digest, as well as producing some vitamins.
We have always been told by healthcare professionals and nutritionists that fiber is important to a healthy diet.
But new research examines exactly what happens if our intestinal microbes do not receive the appropriate amount of fiber.

Studying the behavior of gut bacteria in mice

The study was carried out by an international team of researchers led by Eric Martens, Ph.D., associate professor of microbiology at the University of Michigan Medical School, and Mahesh Desai, Ph.D., from the Luxembourg Institute of Health.
Researchers bred mice especially for the study. Mice were born and raised without any gut bacteria of their own. They then received a transplant of 14 bacteria that normally live in the human gut.
Knowing the genetic signature of each bacterium, scientists were able to track the evolution of each one of them over time. They used a germ-free lab facility and genetic techniques that allowed them to see what bacteria were present and active under different dietary conditions.
Researchers infected the mice with a strain of bacteria that is the equivalent of E. coli in humans. Then they examined the impact of diets with varying amounts of fiber, as well as a diet with no fiber at all.
Researchers tried a diet that was 15 percent fiber, made from minimally-processed grains and plants. They also tried a diet that was rich in prebiotic fiber - a purified form of soluble fiber that is similar to what some processed foods and dietary supplements contain.

Gut microbes really need their fiber

As revealed by the study - published in the journal Cell - the induced infection did not fully spread in mice that received the 15 percent-fiber diet. Their mucus layer remained thick, protecting them against the infection.
But when scientists replaced the diet with one that lacked fiber altogether, gut microbes started eating the mucus. Even a few days of fiber deprivation led the bacteria to start invading the colon wall.
Gut microbes rely on fiber for their food, and when they do not get it, they start eating away at your gut. This makes the gut more prone to infections.
The diet rich in supplement-like prebiotic fiber had the same results as the diet lacking fiber completely. The mucus layer started eroding as a result of the action of microbes.
"The lesson we're learning from studying the interaction of fiber, gut microbes and the intestinal barrier system is that if you don't feed them, they can eat you."
Eric Martens, Ph.D.
Researchers were also able to see what fiber-digesting enzymes the bacteria were making. They found 1,600 different enzymes that digest carbohydrates - a complexity similar to the one found in the human gut.
A lack of fiber also triggered a higher production of such mucus-degrading enzymes.
Scientists were able to look at images of the "goblet" cells on the colon wall that produce mucus. They could clearly see how the mucus layer got progressively thinner as the mice received less fiber.
In a normal gut, mucus is being produced and degraded at a steady pace. But on a fiber-deprived diet, mucus was degraded at a much higher pace than it was produced.
Examining the gut tissue of infected mice, researchers were able to see inflammation across a wide area of thinning, and even patchy tissue.
Infected mice that received a diet rich in fiber also displayed inflammation but across a much smaller area.

Future research to study different diets

In the future, Martens and Desai hope to study the effect of different prebiotic combinations over a longer period of time, as well as the impact of an intermittent natural fiber diet.
Researchers would also like to find the biomarkers that signal the state of the mucus layer in human guts, such as the number of mucus-degrading bacteria.
Martens and Desai also wish to study the impact of a low-fiber diet on chronic illnesses such as inflammatory bowel disease.
"While this work was in mice, the take-home message for humans amplifies everything that doctors and nutritionists have been telling us for decades: Eat a lot of fiber from diverse natural sources.
Your diet directly influences your microbiota, and from there it may influence the status of your gut's mucus layer and tendency toward disease. But it's an open question of whether we can cure our cultural lack of fiber with something more purified and easy to ingest than a lot of broccoli."
Eric Martens, Ph.D.
Learn about how sleep loss can alter the gut microbiota.
Written by Ana Sandoiu