Health Hazards of Low-Fiber Diets Linked to Its Influence on Microbiome

Story at-a-glance

  • Low-fiber diets can cause as much as 60 percent of microbe species in your gut to go extinct, and this altered gut flora gets passed on to future generations
  • As a general rule, people who eat a more plant-based diet and fermented foods tend to have a more diverse gut microbiome than those who skimp on fresh veggies and fruits and eat more processed foods
  • Some of the factors that affect your gut microbiome include diet, exercise, vaginal birth versus C-section, breast feeding, use of antibiotics and certain heartburn medication


This is an older article that may not reflect Dr. Mercola’s current view on this topic. Use our search engine to find Dr. Mercola’s latest position on any health topic.

By Dr. Mercola

Dietary fiber may be far more important than previously imagined.

According to a report1 funded by the Council for Responsible Nutrition Foundation (CRNF), were American adults over the age of 55 with heart disease to take psyllium dietary fiber every day, it could save the healthcare system nearly $4.4 billion a year.

The effect may be even greater than that though, as new research reveals lack of fiber in the diet may impact not just your health, but that of your children and even great-grandchildren too.

How's that, you might ask? By changing the diversity of bacteria in your, and your offspring's, gut.

Low-Fiber Diet Promotes Extinction of Gut Bacteria

The study2,3,4 in question found that low-fiber diets cause "waves of extinction" in the gut of mice, and that this altered gut flora gets passed on to offspring. As much as 60 percent of the microbe species suffered severe decline in the low-fiber group.

In some cases their numbers remained low even after the mice were again given high-fiber meals, suggesting it can be quite difficult to repopulate certain gut bacteria once they've been severely diminished.

Each successive generation of offspring in the low-fiber group also ended up with less diversity than their parents, suggesting the problem compounds over generations. According to the authors:

"[O]ver several generations, a low-MAC diet [microbiota-accessible carbohydrate diet] results in a progressive loss of diversity, which is not recoverable after the reintroduction of dietary MACs.

To restore the microbiota to its original state requires the administration of missing taxa [editor's note: i.e. fecal transplant] in combination with dietary MAC consumption."

Previous studies5 have already confirmed that the human microbiome has undergone significant changes over the course of history, along with changes in diet.

Distinct differences in the gut microbiome have also been found between Western city-dwellers and rural villagers and indigenous hunter-gatherers, and, according to the authors: "The data we present also hint that further deterioration of the Western microbiota is possible."

As a general rule, people who eat a more plant-based diet tend to have a more diverse gut microbiome than those who skimp on fresh veggies and fruits and eat more processed foods.

Smaller Stools Mean Bigger Hospitals

As noted by The Atlantic,6 the late Dr. Denis Burkitt — an Irish missionary surgeon — was ahead of his time. After World War II, Burkitt moved to Uganda, where people ate a very fiber-rich diet, and didn't suffer the high rates of chronic disease, including heart disease and colon cancer as their Western peers.

Burkitt is quoted7 as saying: "America is a constipated nation. If you pass small stools, you have big hospitals."According to Stanford University microbiologist Justin Sonnenburg, Burkitt "nailed it" when it comes to the health benefits of a fiber-rich diet and the dangers of a fiber-deficient one.

The reason for fiber's potent impact is not just related to its ability to improve the passing of stool. It has to do with the fact that it feeds beneficial gut microbes, which in turn play many important roles in your health.

For starters, fiber fuels beneficial bacteria to produce short chain fatty acids that help regulate your immune function. These fats and ketones help increase T regulatory cells, specialized immune cells that help prevent autoimmune responses and more.

Via a process called hematopoiesis, they're also involved in the formation of other types of blood cells in your body. Few Americans get the recommended 30 to 32 grams of fiber per day, and when fiber is lacking, it starves these beneficial bacteria, thereby setting your health into a downward spiral.

Not only does it have an adverse effect on your immune system, allowing autoimmune diseases to set in, lack of fiber in your diet can also lead to the breakdown of your gut barrier, resulting in leaky gut and related health problems.

Leaky Gut Is Real, and a Major Contributor to Allergies

In the past, there have been questions about whether leaky gut syndrome is a "real" condition or not.

Recent research8 has confirmed the reality of leaky gut, showing that, indeed, physical gaps between the cells that line your intestinal barrier can develop, which allow undigested food particles into your blood stream.

A gut protein called zonulin regulates the opening and closing of these holes in the cell wall of your intestine.

When a gap develops, larger molecules such as food particles can get through, thereby causing allergic reactions and other problems such as type-1 diabetes, Celiac disease, Crohn's disease, and irritable bowel syndrome.

Allergies Also Linked to Altered Lung Bacteria

Interestingly enough, recent research has also found that certain bacteria help regulate immune function in your lungs — a place that has previously been considered quite sterile.  As reported by Medical News Today:9

"While most previous studies have focused on how this relationship works in the digestive system, the new study looks at how bacteria in the lungs influence the immune system through specialized cells called dendritic cells ...

The researchers propose that by revealing an important link between antibiotic use, the breakdown in the body's important relationship with the microbiome, and reduced production of IgA [immunoglobulin A] in the lungs, their study points to a new mechanism behind the rise in allergic disorders."

Natural Birth and Breastfeeding Start Babies Off Right

According to Sonnenburg10 who conducted the fiber study on mice: "Everybody accepts that we pass on our human genes to our children, but what we really need to think about and consider is our children inherit a microbial set of genes from us." Indeed, your microbial makeup is influenced directly from birth, with much of it being transferred to the baby as it travels through the birth canal.11

Aside from a flawed diet, the dwindling popularity of vaginal birth plays a significant role in the dwindling microbe species found in people born and raised in developed nations. While C-sections have a number of acknowledged risks, their negative effects on infants' guts due to lack of bacterial exposure is typically overlooked entirely.

This is tragic, as your baby's gut microbiome has the potential to impact his or her health for life. Babies born by C-section have an increased risk for asthma, obesity and Type 1 diabetes, for example. Lack of breastfeeding worsens matters further. Human breast milk contains oligosaccharides (unique complex chains of sugars) that promote healthy gut flora, which are completely absent in commercial infant formulas.

Breastfeeding has been shown to be protective against the very same health problems associated with caesarean delivery. When both vaginal birth and breastfeeding are lacking, your child can end up with severely compromised gut flora.

Abnormal Gut Flora May Predispose Your Child for Neurological Dysfunction

Research by Dr. Campbell-McBride has revealed that nearly all mothers of autistic children have abnormal gut flora. Again, this is significant because newborns inherit their gut flora from their mothers at the time of birth. Establishing normal gut flora in the first 20 days or so of life plays a crucial role in the maturation of your baby's immune system.

According to her research, babies who develop abnormal gut flora also have a higher risk for suffering vaccine reactions. If your baby has suboptimal gut flora, vaccines can become the proverbial "last straw" — the trigger that "primes" his/her immune system to develop chronic health problems, including autism.

I believe Dr. Campbell-McBride's Gut and Psychology Syndrome (GAPS) Nutritional Program is vitally important for most people, but it's particularly crucial for pregnant women and young children.

According to Dr. Campbell-McBride, in children with GAPS, the toxicity flowing from their gut throughout their bodies and into their brains continually challenges their nervous system, preventing it from performing its normal functions and processing sensory information.

Based on such information, I believe maintaining optimal gut flora by eating raw food grown in healthy, organic soil and "reseeding" your gut with fermented foods and probiotics (this is essential when you're taking an antibiotic), may be one of the most important steps you can take to improve your health and your baby's during pregnancy.

Early Exercise Alters Gut Microbes and Promotes Healthy Development

Early activity can also be helpful. Surprising as it may sound, researchers have discovered that exercise during childhood promotes healthy brain development and metabolism in part by altering your gut microbiome.12 As reported by Science Daily:13

"[T]he researchers found that gut microorganisms are especially 'plastic' at a young age ... [J]uvenile rats who voluntarily exercised every day developed a more beneficial microbial structure, including the expansion of probiotic bacterial species in their gut compared to both their sedentary counterparts and adult rats, even when the adult rats exercised as well.

The researchers have not, as of yet, pinpointed an exact age range when the gut microbe community is likeliest to change, but the preliminary findings indicate that earlier is better. A robust, healthy community of gut microbes also appears to promote healthy brain function and provide anti-depressant effects ...

'Future research on this microbial ecosystem will hone in on how these microbes influence brain function in a long-lasting way,' said Agniezka Mika ... lead author of the new study."

Other research, summarized in the video above, found that athletes have a higher diversity of gut microbes compared to inactive control subjects.

One particular species of bacteria called Akkermansiaceae, found in greater amounts in the athletes' gut, has been linked to reduced risk of obesity and systemic inflammation. Granted, there were also significant differences in the diets of the two groups.

The athletes not only ate a more varied diet than the controls, they also ate more protein, fruits and vegetables, and consumed fewer snack foods. According to the authors: "Our findings indicate that exercise is another important factor in the relationship between the microbiota, host immunity and host metabolism, with diet playing an important role."

Antibiotics May Usher In Other Serious Infections

As you can see, a number of factors contribute to the diversity and population size of beneficial gut bacteria, starting with vaginal birth and breastfeeding. Then, from an early age, a diet of real food rich in soluble plant fiber, along with physical exercise, will help maintain a microbiome that promotes health and normal weight. 

But there are also a number of modern-life factors that can counteract all the good you've done. As you likely know, antibiotics are indiscriminate killers, and are lethal to both beneficial and harmful bacteria.

Recent research also reveals that antibiotics can promote secondary infections, by the fact that they render your gut microbiome more vulnerable — and it takes just one course of antibiotics to increase your risk of serious infections such as Clostrium difficile (C. diff), which kills about 14,000 Americans each year.

In an effort to learn more about the mechanisms involved, the researchers compared the intestinal contents of mice, before and after treatment with various antibiotics. As reported by The University Herald:14

"Bacteria in our gut help with the digestive process, fermenting carbohydrates and absorbing fat acids ... An antibiotic treatment may affect the liver by preventing the production of bile acid. Lack of bile can kill bacteria, leading to infection and digestive problems.

The primary bile acid produced by the liver enters the large intestines and becomes secondary bile acid that fights against the C.difficile. The lack of bile acid makes one vulnerable to infections caused by Clostridium difficile bacteria ... A probiotic counters the negative effects of the antibiotic by helping the liver create bile acid to fight against the bad bacteria."

Other research15,16,17,18 has shown that antibiotics raise your risk of contracting drug-resistant infections. According to the authors:

"Among the antibiotics tested, exposure to amoxicillin ... samples had the highest number with antibiotic resistance-associated genes and the most classes that were increased in the predicted metagenomes and in the full metagenomes, respectively, a week after the exposure ... Clearly, even a single antibiotic treatment in healthy individuals contributes to the risk of resistance development ..."

Beware: Heartburn Pills Also Harm Your Gut Bacteria

A British study19 on twins suggests that heartburn pills known as proton pump inhibitors (PPIs) may also increase your risk of bacterial infections  — again by altering your gut flora. As reported by Reuters:20

"Looking for clues to how PPIs might lead to infections, researchers compared stool samples from more than 1,800 British twins. When only one twin used PPIs, their fecal analysis turned up much more Streptococcaceae, a family of bacteria that includes Streptococcus and Lactococcus strains, and that typically inhabits the mouth and skin. Their increased numbers potentially make certain infections more likely, the researchers conclude ..."

Scientists Turn to Probiotics to Improve Plant Growth and Food Safety

The importance of microbes is starting to be recognized in other fields besides human health and medicine. In related news, you find that microbes added to seeds may boost crop production, and some believe probiotics could be instrumental for saving the shellfish industry.

As reported by Scientific American,21 scientists have already begun testing more than 2,000 microbial seed coatings, planted on some 500,000 test plots in the U.S., noting that:

"Communities of soil-dwelling bacteria and fungi are crucial to plants. They help plants take up nutrients and minerals from the dirt and can even extend root systems, providing more access to food and water. They also help plants grow, cope with stress, bolster immune responses and ward off pests and diseases."

Monsanto and Novozymes, through their BioAg Alliance, recently concluded the world's largest field-testing of seeds coated with various microbes. While this is certainly a step in the right direction, it's still worth noting that such technology would be superfluous were farmers to simply revert back to regenerative agriculture  practices.

Seed coatings may improve crop production temporarily, or to a point, but to ensure sustainable food production, we still have to focus on overall soil health. Seed coatings simply won't go far enough, although I certainly see why Monsanto and other companies want to pursue it, as it would be yet another profit stream from patented seeds.

As for the shellfish industry, antibiotics for this industry are not approved for use in the U.S., and infections can spread rapidly and with devastating effects. At present, infections kill 10 to 20 percent of the Northeast's oyster and lobster larvae each year. Here, probiotics are showing great promise,22 helping the larvae fight off bacterial infections while in the hatchery.

Final tests are currently underway, and if all goes well (and the U.S. Food & Drug Administration's (FDA) grants approval), the probiotics may be available for hatcheries within the next two years. Scrambling for alternatives to antibiotics, some chicken producers are also resorting to beneficial bacteria. Perdue Farms is one. As previously reported by NPR:23

"The idea is, all these 'good bacteria' can crowd out the harmful microbes that make a chicken sick. [Perdue executive] Stewart-Brown says that he was initially skeptical about probiotics. 'Eight years ago, I would have said that they're not working in poultry. They're not very useful. Today, I'm saying that they are useful. Expensive, but useful.' Chickens that got probiotics stayed healthier and grew faster than birds that didn't."

The Importance of Fiber for a Healthy Microbiome

Getting back to where we started, one of the quickest and easiest ways to improve your gut health is by eating REAL food, along with traditionally fermented foods.

Mounting research suggests that a high-fiber (especially soluble fiber) diet can help reduce your risk of premature death from any cause, likely because it helps to reduce your risk of a number of chronic diseases. This includes type 2 diabetes, heart disease, stroke, and cancer.

Some of the microbes in your gut specialize in digesting the soluble fibers found in legumes, fruits, and vegetables, and the byproducts of this fermenting activity help nourish the cells lining your colon, thereby preventing leaky gut and related health problems.

Some of these fermentation byproducts also help calibrate your immune system. Avoiding sugar and processed food is equally important, as they promote the growth of fungi and other harmful microbes that can easily take over, given the chance.

Besides diet, other lifestyle factors such as exercise and drug use can have an impact, for better or worse. Pregnancy decisions such as whether or not to have an elective C-section and breastfeeding can also have long-term health effects for your child — all because of how these decisions affect your child's microbiome.

When it comes to fiber, the U.S. Department of Agriculture recommends getting 14 grams of fiber per 1,000 calories consumed. A more general recommendation is to make sure you get 20 to 30 grams of fiber per day. I believe about 25 to 50 grams per 1,000 calories consumed is probably a better goal. Healthy sources of soluble and insoluble fiber include:

Psyllium seed husk, flax hemp, and chia seeds


Vegetables such as broccoli and Brussels sprouts

Root vegetables and tubers, including onions, sweet potatoes, and jicama



Green beans




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