Do you eat too little fiber? This is how you damage your microbiome and increase your risk of disease

Eating too little fiber damages your microbiome and immunity. Replacing whole grains with refined ones increases the risk of digestive problems and chronic diseases....

Table of Contents

1. What happens in your body when you replace whole foods with refined ones
2. Fiber: much more than “to go to the bathroom properly”
3. Low-fiber diet: digestive problems and risk of chronic disease
4. Why refined products and fiber supplements are not the same
5. How to increase fiber with whole foods without discomfort
6. Transform your health starting with what’s on your plate

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The replacement of whole foods with refined products has dramatically reduced the intake of dietary fiber and other protective compounds. That apparent “detail” has profound consequences: more digestive discomfort and a higher risk of chronic diseases, according to numerous nutrition and microbiome specialists.

What happens in your body when you replace whole foods with refined ones

When a cereal is refined, the bran and part of the germ are removed—precisely the fractions richest in fiber, vitamins and bioactive compounds. What remains is basically rapidly digested starch.

When this change is made systematically, from whole-grain breads and rice to white bread, cookies, pastries, sugary cereals and snacks, your body goes from receiving a steady flow of fiber to practically “drying out” of this nutrient.

That decline is not minor: it is estimated that up to 97 percent of adults do not meet daily fiber recommendations, which, depending on age and sex, are approximately between 25 and 34 grams per day. Put simply, that means almost everyone consumes less than their digestive system needs to function smoothly and to protect itself from inflammatory processes.

In the scientific literature fiber has even been considered a “nutrient of concern for public health”, because its deficiency is consistently associated with more chronic diseases and a poorer quality of life.

A curious fact: traditional populations that barely consume refined products can ingest more than 80 grams of fiber per day, with very low rates of constipation, diverticulosis and colorectal cancer.

Quince: a little-eaten food that is high in fiber

Fiber: much more than “to go to the bathroom properly”

The term fiber actually encompasses a whole family of complex plant carbohydrates, with different structures and functions. In general, two major groups are discussed:

• Soluble fiber: dissolves in water and forms a sort of gel. Classic examples are the beta-glucans found in oats and barley. This fiber:
• Helps reduce blood cholesterol
• Increases the feeling of fullness
• Helps stabilize blood glucose

• Insoluble fiber: does not dissolve in water and increases the bulk of the fecal bolus. It is found in nuts, legumes, whole grains, some vegetables and the peel of many fruits. Its main function is to facilitate intestinal transit and prevent constipation.

Both types are essential. Some fibers, especially certain soluble ones, are fermented by bacteria in the large intestine. As a result, short-chain fatty acids are produced, such as butyrate, acetate and propionate. These compounds:

• Nourish colon cells
• Improve the absorption of certain minerals
• Decrease local and systemic inflammation
• Help regulate the immune response

In fact, several researchers highlight that many common diseases in industrialized societies are related to a chronic inflammatory state and immune system dysregulation that, in part, originate in a fiber-poor gut with an impoverished microbiome.

Another striking aspect is fiber’s ability to act like a sponge or matrix that traps unwanted substances. Recent studies indicate that a diet rich in fiber can help eliminate environmental toxins, such as certain microplastics, facilitating their expulsion in the stool. Fiber, in this sense, functions as an additional barrier against everyday pollution.

Low-fiber diet: digestive problems and risk of chronic disease

When fiber intake falls because refined products are prioritized, the impact is felt on several levels.

In daily life, the most visible consequences are usually digestive:

• Persistent constipation or alternation with diarrhea
• Sensation of heaviness and abdominal bloating
• Greater tendency to hemorrhoids and anal fissures
• More frequent appearance of diverticula
• General discomfort after meals

In nutrition education programs in which I have participated as a virtual advisor, it is common for people who base their diet on white bread, snacks, sugary drinks and fast food to report a similar pattern: they go to the bathroom every few days, with effort, pain and much frustration. When whole foods and more vegetables are gradually introduced, the improvement in intestinal transit is often described as “surprisingly quick.”

Beyond the gut, chronic fiber deficiency is associated with an increased risk of:

• Obesity and difficulty regulating appetite
• Type 2 diabetes and insulin resistance problems
• Cardiovascular disease, due to alterations in lipids and blood pressure
• Colorectal cancer
• Higher incidence of chronic inflammatory diseases and some autoimmune conditions
• More allergies and disorders linked to an unbalanced immune response

Books on the microbiome and gut health, such as those written by researchers who study the relationship between diet, gut bacteria and immunity, agree on one central point: a diet rich in plant-based fiber is consistently associated with less inflammation and a lower risk of multiple chronic conditions.

An interesting detail is that fiber also influences mood. Through the gut–brain axis, the metabolites produced by bacteria when fermenting fiber modulate neurotransmitters and substances involved in the perception of stress and anxiety. People who improve their eating patterns by increasing fruits, vegetables, legumes and whole grains often report not only better digestion, but also greater mental clarity and better emotional stability.

Why refined products and fiber supplements are not the same

The decline in fiber intake in recent decades is closely linked to the rise of ultra-processed foods. The refining of wheat, rice and other cereals, as well as the production of snacks, cookies and sugary drinks, has meant that most calories come from products with very little or no fiber.

In response, the market has offered supplements and “fortified” foods with added fiber: bars, yogurts with added fibers, drinks with inulin, among others. They usually use isolated ingredients such as:

• Psyllium
• Methylcellulose
• Inulin and fructooligosaccharides

While some of these supplements can be useful in specific contexts, studies on their effectiveness are variable. In general, results depend on the type of fiber, the dose and, above all, the characteristics of the person’s microbiome. Robust clinical trials and systematic comparisons between supplemental fiber and fiber from whole foods are still lacking.

In addition, concentrated fibers, especially in liquid form or in large amounts, can cause:

• Intense bloating
• Excess gas
• Diarrhea or very soft stools
• Increased intestinal sensitivity in predisposed individuals

One reason is that liquids with fiber pass through the digestive tract faster than solid foods rich in fiber, which can trigger symptoms in people with sensitive guts.

On the other hand, isolated fiber lacks the nutritional complexity of a complete plant food. A legume, for example, not only provides fiber but also:

• Plant proteins
• B vitamins
• Minerals such as iron, magnesium and potassium
• Antioxidant phytonutrients
• Different types of fiber combined in the same matrix

Something similar happens with an apple with skin, a raw carrot or a handful of nuts. No supplement can exactly reproduce that symphony of nutrients and bioactive compounds. Experts’ recommendation is clear: supplements can be a temporary aid, but the foundation should always be fiber from real plant foods.

How to increase fiber with whole foods without discomfort

Increasing fiber does not mean switching overnight to a perfect diet. In fact, abrupt changes can cause discomfort. The key is a gradual, realistic progression. Some practical strategies:

• Increase fiber little by little
Start by adding an extra serving of fruit or vegetables a day and, every few days, add a new fiber source. This gives your microbiome time to adapt.

• Drink enough water
Fiber, especially insoluble fiber, works better with adequate hydration. Without water, it can worsen constipation instead of relieving it.

• Prioritize whole foods at every meal
• Breakfast: oats, whole-grain bread, fresh fruit with skin, chia or ground flax seeds
• Lunch and dinner: half a plate of vegetables, a serving of legumes several times a week, whole grains such as brown rice, quinoa or barley
• Snacks: fruit, nuts, homemade popcorn with little oil and no added sugars

• Seek plant variety
Research shows that people who consume more than thirty different types of plants per week tend to have a more diverse gut microbiome. You don’t need to obsess over counting, but it’s useful to aim for variety: different fruits, vegetables of all colors, varied legumes, nuts and seeds.

• Choose affordable options
It’s not necessary to rely on expensive products. Some inexpensive, fiber-rich options are:
• Frozen fruits for smoothies or simple desserts
• Dried or canned legumes, well rinsed before eating
• Avocado, which provides fiber and healthy fats
• Chia and flax seeds, easy to add to yogurt, salads or soups

In food education initiatives, many people discover that by replacing some refined products with these simple options, they not only improve digestion but also notice more sustained energy throughout the day and fewer sugar cravings.

Transform your health starting with what’s on your plate

The replacement of whole foods with refined products has emptied much of modern diets of fiber and protective nutrients. That deficit contributes to common digestive complaints and to an internal environment more prone to inflammation and chronic disease.

At the same time, the accumulated evidence points to something very encouraging: bringing whole, varied plant foods back to the plate has a profound and positive impact on the microbiome, the immune system, metabolism and emotional well-being.

In talks on gut health education a simple but powerful idea is repeated: each time you choose a whole fruit instead of a sugary juice, a whole-grain bread instead of white bread, homemade legumes instead of an ultra-processed dish, you are sending a clear message to your body and your microbiome: “I want a less inflamed, more resilient terrain with better defenses against disease.”

It’s not about perfection, but about direction. Starting with small, sustained changes—prioritizing whole, fiber-rich plant foods and progressively reducing refined products—can make the difference between a gut that barely “survives” and one that truly thrives, supporting your long-term health.

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