Sugar and Gut Health: What You Need to Know
15 minute read

Sugar and Gut Health: What You Need to Know

Many of us are familiar with the belly aches that come after a night of excess sweets. It’s easy to recognize the effects of sugar when ingestion, bloating, or an urgent trip to the bathroom immediately follows a donut binge.

The connection between sugar and other maladies, such as fatigue, headaches, hormone imbalance, anxiety, and acne may be harder to spot, even brushed off as “unrelated,” especially when we think we’re consuming less sugar than we actually are. Sugar is cleverly hidden in many of our favorite pantry staples, playing a silent, but big role in our everyday ailments.


The Gut Microbiome

In order to understand our health, we need to understand gut health. And in order to understand gut health, we need to understand the gut microbiome, an ecosystem of bacteria, viruses, and fungi that resides in our gut (our colon, to be exact). These beneficial bugs perform essential functions that protect our overall health.

The microbiome bacteria have protein-encoding genes, just like humans have genes. The difference is, humans have roughly 23,000 genes, whereas each human’s unique microbiome contains roughly 3.3 million unique protein-encoding genes.[1] We’re just a small vessel for the vast universe that lives inside us.

The microbiome is, in a way, its own organ, made up of trillions of microbial cells. Collectively, it weighs around 4 lbs![2] But before you dismiss these bacteria as dead weight, consider that they are to thank for some of the hardest jobs in keeping us healthy: protecting immunity, fighting off pathogens, synthesizing vitamins, and producing short-chain fatty acids which nourish the cells in the colon and reduce risk of inflammatory diseases.[3]


Where Does the Microbiome Come From?

The human microbiome develops from the moment a baby is born. The baby swallows bacteria on its way out of the birth canal and continues to ingest more bacteria through breast feeding. During the first few years of a child’s life, their microbiome continues to develop with exposure to dirt, people, pets, and new foods.


Feeding Time

The beneficial bacteria that make up our microbiome need to be fed, just like we do. And just like us, what we feed the bacteria can make all the difference in how they grow. Their health, strength, and diversity are highly influenced by the foods we eat (and don’t eat).

A healthy microbiome is a balanced one – it contains beneficial bacteria as well as harmful bacteria, or pathogenic bacteria. This is normal, and in healthy individuals the beneficial bacteria keep the pathogenic bacteria in check and prevent them from creating disease.

However, diets high in sugar and low in dietary fiber feed these pathogenic bacteria while starving out the good bacteria, leading to dysbiosis, an imbalance. If dysbiosis goes on too long, it can lead to illness. On the other hand, foods low in sugar and high in dietary fiber feed the beneficial bacteria and starve out the harmful ones.


Digestion in Action

Let’s zoom out to understand where these friendly bacteria live and how they work in the digestive process.

Digestion starts in the mouth before you take your first bite of food. Just the sight and smell of food make your salivatory glands secrete saliva in anticipation. Enzymes in the saliva help break down the food while it’s being chewed.

Muscular contractions called peristalsis push food down the esophagus and into the stomach, which holds the food for roughly two hours while more enzymes and stomach acid break it down more.

While food is in the small intestine, the pancreas releases pancreatic enzymes to continue the process, as well as insulin, a hormone that converts sugar into glucose for energy. The liver breaks down and removes toxins and the gallbladder releases bile to help digest fats.

Once the food is reduced to molecules, the small intestine absorbs nutrients from the food and moves those nutrients into the bloodstream. Thirty-six (36) hours since your first bite, it’s on to the large intestine (the colon) where the waste from all this food gets prepped to leave the body - but not before the beneficial bacteria interact with it!

Fiber is unable to be broken down by the body itself during the digestion process. Rather, the bacteria in the colon feed off the fiber and break it down. These friendly bugs also synthesize vitamins from the food. When the colon is full of waste it empties into the rectum, and soon after, gets evacuated.[4]

Quite an adventure!


A Sugar Epidemic

On average, U.S. adults consume 22 teaspoons of sugar every day (children consume 32 teaspoons daily). You may be shaking your head thinking, “There’s no way I eat that many teaspoons of sugar a day!” Between processed foods and sugary beverages, most of us do.

Teaspoons are measured by the number of grams divided by four, i.e., if your frozen dinner contains 20 grams of sugar, that’s five teaspoons right there. The average can of soda contains eight teaspoons of sugar alone. It adds up and creates a considerable challenge before us.

According to the American Heart Association, this average daily sugar intake is two-four times more sugar than the recommended limit. That limit is:

  • 9 teaspoons for men
  • 6 teaspoons for women
  • Up to 8 teaspoons for children[5]


How did we get here?

In 1973, corn farmers received subsidies from the Farm Bill, a legislative package of guidelines for farmers and crops. As a result of the subsidies, corn farmers started producing an abundance of corn and corn became cheaper.

Soon after, farmers realized they could make high-fructose corn syrup (HFCS) from corn. It was sweeter and cheaper to produce than sugar, and it yielded more profits for the farmers. Food companies quickly caught on to the addictive, inexpensive value of HFCS, not to mention, its ability to give baked goods a longer shelf life. Pretty soon, most of our food supply contained HFCS.[6]

To add insult to injury, a few years later the war on fat began. It started when the Senate Select Committee on Nutrition and Human Needs recommended a 10% reduction in dietary fat. Food companies scrambled to remove fat from their products (adding in sugar to compensate for taste) and started to point the weight gain blame on dietary fat.[7]

Consumers began to fear fat and food companies took advantage. Fat, not sugar, continued to take the blame for obesity for many years to come. In the meantime, our collective health began to plummet.


Sugar’s Sneaky Hiding Places

When consumers caught on to the harmful effects of sugar, including its links to weight gain, damage to the microbiome, and inflammatory diseases (type 2 diabetes, heart disease, Alzheimer’s), the food industry had to act fast. Unfortunately, their choice actions did not do us any favors.

Rather than remove or reduce sugar from their products, they created clever advertising slogans and alternative names for sugar to throw us off their scent. For example, by replacing sugar with molasses, a food label can claim the product is “sugar-free” even though molasses is just another form of sugar.

Labels also try to distract us by calling attention to other things. A product may be “gluten-free,” “natural,” “soy-free,” or “healthy,” but these terms say nothing about the sugar content.

In fact, in the U.S., the word “Natural” can be used freely on products without any standards, except for meat and poultry. Once again, these terms are used on food packaging regardless of sugar content or actual health benefits.

Sugar, or other versions of it (HFCS, honey, agave), is added to many processed and packaged foods, even ones you would never expect:

  • breads and pastas
  • cereals
  • crackers
  • yogurt
  • dressings
  • sauces
  • dried fruit
  • condiments
  • nut butters and jams
  • canned soups
  • deli meats
  • frozen meals

This added sugar (not to be confused with the naturally occurring sugars that exist in all fruits, vegetables, and grains) is problematic. Naturally occurring sugars from plant foods come hand-in-hand with fiber, vitamins, and other nutrients.


Sneaky Sugar Names

Sugar by any other name would taste as sweet, sometimes sweeter. And unfortunately, sugar by any other name metabolizes the same way in the body as sugar and can lead to the same illnesses. Check out some of the alternate sugar names companies use on food labels.


How Sugar Affects the Gut and Beyond

Sugar has numerous effects on the body by way of the gut. The intestinal wall is only one (1) cell thick, and it’s all that stands between harmful food particles/toxins and our blood stream. Sugar can damage our gut wall, as well as our cells, organs, and tissues. It also alters and impairs our microbiome. This combination can cause a cascade of health problems that, at first glance, may seem unrelated to gut health. Let’s look a little closer.


Leaky Gut (a.k.a. Increased Intestinal Permeability) and Inflammation

Our gut lining is meant to be permeable – it has to be to allow nutrients to enter the blood stream – it just can’t be too permeable. One of the most important jobs our gut bacteria have is to camp out at the gut lining and act as border guards to make sure only nutrients (not toxins or food particles) come through.

Our microbiome thrives on nutrients, especially dietary fiber, probiotics, and prebiotics. But when we consume too much sugar, we feed the wrong type of bacteria and decrease our beneficial microbes. This creates dysbiosis which can cause changes to the mucosal lining of the intestines and kill off those bacterial border guards.

When there are changes to the mucosal lining, the intestinal wall can become too permeable or “leaky,” allowing harmful food particles and toxins to enter the bloodstream. And when anything passes through the barrier that isn’t supposed to, it causes the body to launch an autoimmune type of attack (the body attacks itself) – it sees these trespassers as foreign invaders. In the process, inflammation rises which can cause headaches, acne, or digestive distress, and over time, inflammatory medical conditions (obesity, type 2 diabetes, heart disease).

Inflammation is not only linked to disease, it may play a significant role in how we absorb nutrients. The walls of the intestines have layers, and behind the layers is interstitial fluid which lubricates cells, helps transport nutrients, aids in communication between cells, and removes waste. But when the intestines are inflamed, the fluid increases and it makes it harder for nutrients to pass through into the bloodstream.


Skin Issues

The gut and skin are intricately connected. Both are organs which house microbes, designed to protect us from pathogens. When it comes to a good complexion, it’s what goes on inside the gut that determines what shows up on the outside.

Our skin is made up of collagen and elastin. Sugar can negatively interact with collagen, creating less elasticity, making our skin less soft and supple.[8] In addition, sugar’s harm to the gut wall and microbiome is directly correlated with acne and eczema.

Acne is linked to an overgrowth of Propionibacterium acnes, a bacterium which is fed by sugar. Acne has also been connected to low stomach acid.[9] Eczema, a chronic inflammatory skin condition, can be treated by reducing inflammatory foods such as dairy and sugar. Many functional medicine doctors will advise patients to make these dietary changes before prescribing topical creams or steroids. Additionally, many people who suffer with eczema also have leaky gut.[10]


SIBO (Small Intestinal Bacterial Overgrowth) and Candida Overgrowth

SIBO develops when the beneficial bacteria in the colon/large intestine move into the small intestine, where they don’t belong. The bacteria itself isn’t bad, just in the wrong place. The small intestine is meant to be sterile, free from any bacteria (good or bad). When bacteria consume carbohydrates (especially sugar) they turn those carbs into gas, and this process can be painful when it happens in the small intestine.[11]

SIBO can be difficult to cure because even when you kill off the bacteria with antibiotics, more will eventually grow in the colon and can easily migrate back to the small intestine. Treating SIBO is a multipronged approach that should be overseen by a specialist, but one of the best ways to heal from SIBO and reduce symptoms is to avoid sugar.

Similarly, Candida overgrowth (candidiasis) is another type of bacterial imbalance.[12] Candida is a yeast we naturally have on our skin, in our mouth, vagina, and gut. The yeast is not the problem, the overgrowth is. An overgrowth can lead to a vast list of symptoms including oral thrush, sinus infections, weight gain, fatigue, brain fog, anxiety, depression, joint pain, and of course, digestive issues. As with SIBO, Candida is fed by sugar.


Heal Your Gut

Hippocrates understood early on what scientists have taken hundreds of years to figure out: “All disease begins in the gut.” The hallmark of a healthy gut is a healthy microbiome and the easiest place to start healing is by reducing sugar.

In cases of severe GI conditions, therapeutic diets such as the Body Ecology diet (BED), Specific Carbohydrate diet (SCD), Low-FODMAP diet, Bi-phasic diet, and the Gut and Psychology Syndrome diet (GAPS) can be prescribed by doctors to manage symptoms and repair the gut. Each of these diets has unique guidelines, but they have one thing in common: eliminate sugar and refined foods.

These therapeutic diets are not fad or weight loss diets, but rather, temporary medical interventions that are followed under the supervision of a doctor during the healing process.

Luckily, most people won’t need to go to such extremes to heal their gut. By simply reducing sugar and processed foods, the microbiome can rebalance, and the gut can begin to heal. In many cases, not much may be needed beyond that.

Chronic stress can also take a toll on gut health because it continuously raises cortisol. Incorporating stress reduction into your daily routine can help alleviate damage. It’s helpful to take stock of all stress – emotional, mental, physical, chemical, even perceived stress, and remind ourselves to focus only on the stresses we can control and try to let go of the rest. How we manage and react to stress can play a major role in reducing inflammation and improving digestive health.

Supplements may be a helpful addition to a gut repairing regime.

  • Collagen and l-glutamine are especially beneficial for restoring the gut lining.
  • Marshmallow, licorice root, and slippery elm can be helpful in rebuilding mucosal layers in the GI tract.
  • Probiotic and prebiotic supplements may be recommended to rebuild a healthy ecosystem of bacteria.
  • Spices like ginger and cinnamon have soothing capabilities.
  • A doctor may also recommend prokinetics which enhance motility. This is especially important when treating SIBO.

An individual should always consult with their doctor before taking any supplements to ensure there is no contraindication, establish dosages, and determine what’s best for their unique body.



This information is not intended to prevent, diagnose, prescribe, or treat any illness or condition, nor does it take the place of sound medical advice. You should always seek out your own medical care and determine the best diet and course of treatment for your unique health needs.















  • The average daily sugar intake is two-four times more sugar than the recommended limit
  • There are many names for sugar, which is why it can be difficult to detect in food products
  • Poor gut health can lead to leaky gut, skin issues, and SIBO
  • It is possible to heal your gut

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