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Fiber Protects Your Microbiome

September 5, 2016 (Updated: November 5, 2018)
Lily Moran

We all know that fruits and vegetables are the cornerstone of any good diet. They provide us with a multitude of vitamins, minerals, and antioxidants, as well as other beneficial substances like fiber. Most of us are aware that fiber is what keep us “regular,” but it has other important function too. Most notably, adequate fiber intake reduces your risk of conditions like colon cancer, heart disease, diabetes, and even premature death.


Fiber is a carbohydrate. It’s not a starch or sugar, though—it’s actually a structural carbohydrate. It’s the rigid, supportive “scaffolding” of a plant. It’s what makes kale and Swiss chard stand up in the garden, it’s the casing around each individual kernel of wheat and other whole grains that helps preserve its freshness.

There are two types of fiber: soluble (in fruits, vegetables, and nuts) and insoluble (in whole grains, legumes, and vegetables).

Soluble fiber works by absorbing water in the intestines, forming a gel-like substance that gets fermented in the large intestine. In the process, the gut sends messages that tell the brain, “I’m full.”

Insoluble fiber operates a bit differently. It cannot be digested, so it travels through the digestive tract like a scrubbing sponge, collecting waste residue for elimination. Additionally, while soluble fiber sends a message of fullness to the brain, insoluble fiber creates actual, physical fullness so you don’t overeat.

How Bacteria Aid in Digestion

While fiber is edible, it is mostly indigestible by your digestive tract. However, when it arrives in the large intestine, billions of friendly bacteria that live in the gut (probiotics) take over the digestive process.

These friendly bacteria carry enzymes that are necessary to break down the fiber. They then ferment the resultant sugars into a variety of prebiotics (food for the bacteria themselves) and short-chain fatty acids (SCFAs). SCFAs have several important functions, one of which is helping the bacteria nourish and heal the intestine’s delicate lining. Some research even suggests that SFCAs help to temper inflammation not only in the gut, but in other parts of the body.

This whole communication loop between the gut and its resident microbes all depends on ample fiber supply—and it’s an extremely delicate process. When fiber supply is adequate and bacteria are thriving, they send proper signals to the intestinal cells. In turn, the intestine responds by boosting the protective intestinal mucus layer in which bacteria live, and by releasing molecules that kill harmful bacteria that may invade.

However, when fiber intake is too low, your beneficial bacteria starve. The protective mucus lining also starts to diminish, which causes bacteria to dig too deep into the intestinal wall. This results in inflammation—which, if it ends up chronic, can result in a number of diseases.

Recent research has shown just how symbiotic the relationship between fiber and your friendly gut bacteria really is.

In one experiment, researchers put mice on a low-fiber diet. They tested gut bacteria population in the mice by analyzing their feces. What they found is that a diet low in fiber caused the numbers of beneficial microbes to crash—tenfold! Not only did some common species of bacteria become rarer; rare species became more prevalent.

Furthermore, the intestines of the low-fiber diet mice also got smaller, the protective mucus layer became thinner, and bacteria ended up too close to the intestinal wall, triggering an inflammatory immune response. Not only that, the mice gained weight and developed high blood sugar problems.

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The takeaway here is that fiber is an incredibly important part of your diet. Your health—and the health of your entire microbiome—depends on it.

Up Your Fiber

The Food and Drug Administration recommends 25 grams of fiber per day for women and 35 grams for men. For both sexes, at least 6 grams of their fiber intake should be soluble.

Unfortunately, fewer than five percent of Americans eat enough fiber. The average is roughly 17 grams. We clearly have some catching up to do.

Rest assured, fiber-rich foods don’t have to taste like cardboard. On the contrary, some of the most delicious plant-based foods just so happen to be fiber bonanzas. Raw berries contain 4-8 g of fiber per cup, frozen green peas contain 14g per cup, and 1 ounce of nuts contains 1-4 g of fiber. Whole wheat foods, cooked beans, leafy greens, squash, and fruits like bananas, pears, and organs are all great sources of fiber.

Fiber supplements are also an option, but they tend to be made from single, isolated sources and lack the array of different fibers found in whole foods. As a result, they can cause abrupt changes in gut bacteria, which can lead to bloating and gas. This is why your best bet is whole foods.

Boost Your Bacteria, Too

Along with increasing your fiber intake, you should also consider supporting and boosting the beneficial bacteria in your gut with a high quality probiotic supplement.

It is incredibly important to find a probiotic product that has enterically coated or microencapsulated bacteria. This special technology allows delicate bacteria to survive the acidic, unforgiving environment of your stomach, delivering them safely into your digestive tract.

You should look for a product that contains a blend of different strains of bacteria, with at least 10 billion colony forming units (CFUs) per dose. (This refers to the number of live and active bacteria found in each serving.)

One very beneficial family of bacteria is Lactobacillus (which includes acidophilus, rhamnosus, casei, and many others). These lactic acid-producing microbes normally live in the digestive, urinary, and genital systems. Another family, Bifidobacteria (which includes bifidum and longum), is found mainly in the gastrointestinal tract and mouth. All of these strains work together to create a healthy, robust microbiome.

For best results, follow the dosage and storage instructions listed on the supplement label. Some probiotics can be kept in a cool, dry place, while other brands may need to be refrigerated.


Zou J, et al. Fiber-Mediated Nourishment of Gut Microbiota Protects against Diet-Induced Obesity by Restoring IL-22-Mediated Colonic Health. Cell Host Microbe. 2018 Jan 10;23(1):41-53.e4. doi: 10.1016/j.chom.2017.11.003. Last accessed Oct. 24, 2018.

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