by Dr. Bill Rawls
Updated 6/24/19

Gut Dysfunction Causes, Symptoms and Natural Remedies

For many people, the digestive tract is where health problems begin. For one, the type and quality of food we put into our systems is directly correlated to risk of numerous illnesses, and eating is something we do multiple times a day, every single day. That’s a lot of opportunity to get things right — or mess them up.

What’s more, the majority of our immune system tissue resides in the gut. Research has shown that gut-associated lymphoid tissue (GALT) makes up almost 70% of the entire immune system. And about 80% of immunoglobulin A cells — plasma cells that play a key role in immune function — reside in GALT. Which means when the gut isn’t functioning properly, our ability to fend off illness falters, too.

Keep reading to learn more about the top causes and symptoms of gut dysfunction, plus the best natural remedies and lifestyle habits for preventing and reversing GI issues.

Digestive Dysfunction, Defined

Before we talk about digestive dysfunction, it’s helpful to understand what healthy digestive function looks like.

When everything is working normally, eating food stimulates intense acid production. During this reaction, the lower part of the esophagus, called the lower esophageal sphincter (LES), stays tightly constricted to protect the esophagus from acid.

After the acid has done its job of breaking down food, it’s followed by a fairly rapid emptying of the stomach. Once the stomach empties, acidity in the stomach declines, and the LES relaxes.

When stomach function is compromised, however, instead of the normal response, a moderately acidic stew of partially digested food sloshes around in the stomach for much longer than it should. With reduced acidity and slowed emptying, the LES does not constrict properly, and acidic material splashes back into the esophagus, causing burning and irritation (aka, acid reflux). If this occurs chronically, scarring of the lower esophagus can occur.

Irritation and erosion of the stomach lining presents as the classic “heartburn” symptoms along the left side of the upper abdomen. Erosion can also occur at the duodenum, where the stomach empties into the small bowel. This presents as pain in the middle of the abdomen in an area called the “epigastric region,” and can radiate to the back.

Erosions are often associated with a bacteria called H. pylori. While H. pylori is often present in ulcers, the bacterium is simply an opportunist — 40% of people harbor H. pylori as a normal flora.

When ulcerations start to occur, the bacteria, which is already present, starts infecting the wound and aggravating the process. Antibiotics are sometimes indicated, but the processes causing stomach irritation and erosion must be reversed for complete healing.

Moving farther downstream in the digestive tract, dysfunction in the intestines — such as inhibited motility and bacterial overgrowth — compromises the mucosa or protective barrier of the intestine. Once the intestinal mucosa has been totally compromised, foreign proteins “leak” across into the bloodstream in high concentrations.

The foreign proteins then stimulate the immune system into overdrive, triggering antibody production, activating chemical messengers of the immune system, and initiating histamine response (classic allergic response). This increasingly common condition is referred to as leaky gut syndrome.

The Top Causes of Gut Dysfunction

Man stressed while working on laptop

Normal health is not possible without normal digestive function, and unfortunately, there are a number of prevalent stress factors in modern-day life that are making gut dysfunction more common than not. Normal digestion is most often compromised by these three system disruptors:

  • Gut-offending foods
  • Chronic stress
  • Imbalance of the gut microbiome

Gut-Offending Foods

There is no perfect food, and all foods carry at least some potential for harm to the digestive system. That being said, some foods carry a higher potential for harm than others.

By far, the most irritating foods to the gut are seeds, namely grains, beans, and nuts. Think about it: The purpose of any seed is to grow a new plant, not to nourish some other creature. Not surprisingly, plants are equipped with substances that deter consumption.

The primary deterrents are proteins called lectins, which irritate cells that line the intestines of animals. There are many different types of lectins, some more irritating than others.

Lectins are very stable proteins and are only minimally broken down by stomach acid. Extensive boiling will break them down, but not baking. Sprouting and fermenting also helps break down lectins. Of all the grains, wheat contains the most irritating lectins.

Wheat also contains gluten, a family of proteins that supply amino acids to the sprouting plant. Types of gluten vary for different gluten grains (wheat, barley, rye), but gliadin, which is only present in wheat, is the most reactive. Because gluten is foreign to animals, it is very irritating to the gut and very allergenic.

Eating wheat (and other grains) is possible because the intestinal lining is protected by a mucous layer. But when consumption of processed wheat and corn products is excessive or intestinal motility is impaired, the protective layer is stripped away and chronic damage to the intestinal lining occurs.

Wheat also contains starches that, when consumed in excessive amounts, stimulate overgrowth of harmful bacteria in the intestines. Bacterial overgrowth also damages the intestinal lining.

Once the intestinal lining is disrupted, leaky gut can develop, causing an intense immune reaction such that the immune system becomes sensitized to those proteins. If sensitivity is severe, it can result in an autoimmune illness called celiac disease, in which an immune reaction to the gluten protein cross-reacts with small bowel tissue, causing severe inflammation.

Other grains also contain lectins and storage proteins, but are less irritating than wheat. Rice contains the least irritating proteins and is well tolerated by most people.

Bean lectins are also extremely irritating to the gut. Raw beans are actually poisonous. Fermented soybean products are generally tolerated well. Lentils and mung beans are the easiest to digest. All beans should be thoroughly washed, soaked, and boiled before consumption.

Nuts are generally well tolerated by most people, but can cause gut irritation if digestive problems have long been present.

Night-shade vegetables (tomatoes, potatoes, peppers, eggplant) also contain high concentrations of irritating lectins.

All seeds can harbor toxic mold, especially wheat and corn. Any foods, with time (even in the refrigerator) will start growing mold.

Dairy products (with the exception of cultured yogurt/kefir) are notorious for growing toxic mold. Dairy is also a challenge for people who lack the enzyme that breaks down lactose. Milk proteins are also very allergenic for some people.

Meat proteins are not irritating to the gut, but high concentrations of protein can be a challenge to the digestive system. Red meat laden with saturated fat is the hardest to digest. Poultry and fish are easier for most people to digest.

Cooked vegetables are generally the best tolerated of all foods. Cooking (ideally steaming) breaks down fiber and releases nutrients. Cooking also kills mold, microbes, and parasite eggs.

Chronic Stress

It’s important to note that chronic stress is not the same as acute or short-term stress. How so?

When you’re faced with an acute threat, your body goes into high alert. Often called the fight-or-flight response, it prepares the body for dealing with a threat such as a confrontation or emergency. Resources of the body shift toward dealing with the threat. Everyday maintenance and intestinal functions are temporarily placed on hold until the threat passes or is resolved.

In the modern world, the perception of threat is always present; just going about day-to-day life is stressful. People have come to accept chronic stress as a normal part of daily life because they do not know anything different.

Of all systems in the body, the gastrointestinal system is the most affected. Chronic stress inhibits gastrointestinal function and slows the movement of food materials through the gut. Secretion of digestive enzymes is inhibited and the digestive process is compromised. Everything gets backed up.

Slowed emptying of the stomach causes acid to splash into the lower esophagus and cause burning, and the erosive properties of lectin-loaded foods are compounded. Chronic stomach irritation and erosions are a common consequence.

The flow of bile through the liver and gallbladder is slowed. This commonly results in liver congestion and formation of stones in the gallbladder. Removal of toxins from the body is inhibited.

Gut Microbiome Imbalance

Processed food products, mostly made from wheat, corn, and soybeans, are not only loaded with lectins, but also with starch and sugar — much more than the body can use or absorb.

Unfortunately, undigested starches and sugar are fodder for intestinal bacteria. Overgrowth of bacteria in the small intestine (referred to as SIBO, short for Small Intestine Bacterial Overgrowth) results in symptoms of bloating, trapped gas, and chronic abdominal discomfort. And as toxins from bacterial die-off add up, explosive diarrhea can occur.

Starches and sugar also stimulate growth of yeast. Yeast are always present in the intestines, but growth is normally inhibited by friendly bacteria. The presence of undigested carbohydrates allow yeast to flourish. Toxins produced by yeast overgrowth make a person feel terrible all over.

The Top Foods for Supporting Digestive Health

Garlic in bowl and vegetables on table.

An optimal diet for restoring healthy gastrointestinal function should start with lots of lightly cooked vegetables. Steaming or low-heat sauté with minimal oil is best. Grilling and frying should be avoided until digestive health is restored.

Raw food should also be eliminated; all food should be cooked until GI health is restored. Smoothies are an exception because high torque food processors generally break down raw food enough so that it is well tolerated.

Avoid processed carbohydrates (sugar and starchy foods). Red meat consumption should be low. Avoid acidic foods such as citrus and tomatoes. Spicy foods such as hot peppers can irritate an established problem, but are not causative.

As for beverages, coffee is a gastric irritant, and alcohol consumption can aggravate the disease process. Soft drinks are acidic and should be avoided. Even tea is a gastric irritant. Plain water is your best beverage option until healing is complete.

Foods to Fill Up On:

  • Vegetables like squash, spinach, green beans, asparagus, carrots, celery, sweet peas, and mushrooms are helpful for restoring the gut.
  • Cabbage is generally well tolerated, but other cruciferous vegetables (broccoli, cauliflower, Brussels sprouts) are more difficult to digest and cause gas in many individuals; therefore, they’re best avoided until digestive function is in better shape.
  • Vegetables from the onion and garlic family promote growth of favorable bacteria in the intestines.
  • Sweet potatoes are generally well tolerated, but regular potatoes should be minimized or avoided until normal function returns.
  • Temperate fruits (berries, apples, pears, peaches) can be enjoyed, but tropical fruits (oranges, pineapple, mangoes) should be avoided due to their high sugar content.
  • Mung beans and lentils are the easiest beans to digest, but still contain lectins and should be avoided if the digestive tract is in bad shape.
  • Poultry (chicken, turkey) is the best meat option, but non-oily fish is also generally well tolerated. Tofu is acceptable in the absence of soy sensitivity.
  • Avoid dairy products with the exception of cultured yogurt and kefir.
  • Rice and gluten-free oats are the best tolerated grains.

Foods to Avoid:

  • All processed food products
  • Sugar and starchy foods (wheat, flour products, potatoes)
  • Acidic foods (citrus, tomatoes)
  • Coffee and tea (until healing is complete)
  • Spicy foods
  • Dairy (with the exception of cultured yogurt/kefir)
  • Pork and beef
  • Cruciferous vegetables (broccoli, cauliflower, Brussels sprouts)
  • Nightshades (tomatoes, potatoes, peppers, eggplant)
  • Tropical fruits (oranges, pineapple, mangoes)
  • Nuts
  • Soft drinks
  • Alcohol

Restorative Therapies for Overcoming Gut Dysfunction

Green chlorella pills. Top view.

The right restorative therapies go straight to the source of your digestive issues, so your body recovers its ability to heal itself, and symptoms subside. The goal is to restore homeostasis, optimize immune function, and control any threatening microbes Here’s how to put restorative gut therapies to work.

Slippery Elm

Slippery elm contains mucilage, a slick, gel-like substance that naturally soothes sensitive or inflamed tissue in the gut lining. Mucilage also helps recreate the barrier in the gut lining that keeps things like lectins from leaking through.

Digestive Enzymes

A dysfunctional gut can’t produce enough digestive enzymes to break down food at a healthy rate; replacing those enzymes until you can restore your body’s capability to produce them on its own can help reduce stagnant food in your gut and speed your recovery. Digestive enzymes also keep moving any toxins along that aren’t absorbed by your tissues.


Carminatives are herbs with volatile oils that help ease inflammation and relieve painful spasms that contribute to abdominal cramps. They also relax tight tissue in the smooth muscles of your digestive system that can cause constipation. Cardamom and fennel are top choices.

Digestive Bitters

Your tongue, stomach, pancreas, and colon have specific receptors that encourage the production of digestive enzymes, stomach acids, and liver bile that all aid in digestion the minute they taste bitter. To help keep the digestive process going, take bitters with every meal, and supplement with bitter herbs, such as dandelion.


This antimicrobial herb fights the bad microbes and lets the good ones be. Many herbs have antimicrobial powers, but berberine is not absorbed by the intestines when taken orally, so it’s particularly valuable for restoring balance in gut microflora.


Poor gut health usually translates to poor ability to absorb the essential nutrients your body needs to heal and function normally. Chlorella is a freshwater green algae that’s brimming with beneficial nutrients to help replace those you’re missing.

Plus, chlorella is loaded with chlorophyll, a potent antioxidant that binds to toxins in the GI tract and holds them there so they don’t get absorbed. That includes organic-type toxins (herbicides, pesticides, mycotoxins), as well as heavy metals and plastics.

Additional Lifestyle Tips for Improving Gut Health

Homemade Fresh Ginger Tea with Lemon in a Mug

Chew Your Food Thoroughly.

Digestion starts in your mouth. Chewing is the only part of the digestive process over which we have voluntary control. Smaller and more frequent meals allow the stomach to return to normal size.

Eat Like a European.

The American habit of sitting down to a large meal at the end of a stress-filled day encourages gastrointestinal dysfunction. We would all do well to mimic our European neighbors with a midday main meal and a light supper, but most Americans find it hard to make the change.

At the very least, a regular practice of distributing food throughout the day instead of a large end-of-day meal is better for digestion. Avoid eating after 6pm. Relaxing and stretching before a meal is another good practice. Never eat on the run.

Sip, Don’t Chug.

Large amounts of cold liquids consumed with food may slow enzymatic function and impede digestion. Small sips of liquid during a meal are better. Again the Europeans are one up on us with a habit of drinking water, wine, or beer at room temperature (though alcohol should be avoided until healing is complete). Large iced drinks should be reserved for quenching thirst after exercise.

Drink Apple Cider Vinegar Before Meals.

Taking 1-2 tablespoons of apple cider vinegar (diluted in a 6-ounce glass of water) with meals is a simple way to improve digestive function in the stomach. (Note: If stomach ulcers are a concern, digestive enzymes and vinegar should not be used unless instructed by a healthcare professional.)

Drink Ginger Tea.

Consider this to be an essential part of your recovery. Ginger’s healing properties soothe an inflamed stomach and intestinal tract.

Keep Stress in Check.

Moderating stress and regularly practicing relaxation techniques is essential for allowing the gastrointestinal tract to perform its job.

Use Medications Sparingly.

Short term use of medications to reduce acid can allow healing of the lower esophagus, but acid-reducing drugs should never be your only strategy. Treatment with acid-reducing medications neutralizes acid and reduces symptoms of esophageal burning, but does not eliminate the actual reflux. These drugs actually compromise digestion even further.

Chronic use of these drugs also carries the problem of accelerated bone loss and increased allergies and food sensitivities. These drugs should not be used long term. Here are some general guidelines to follow:

  • Use standard OTC antacids for burning until the burning no longer occurs.
  • Use acid reducing medications only as necessary. This should not be your primary therapy. Start with moderate acid reducers like Zantac or Pepcid first, and only use stronger acid reducers like Prilosec and Nexium if absolutely necessary.
  • Pepto Bismol is effective for reducing burning and encouraging healing (but it will turn stools very dark).

The guidelines outlined here should be followed until digestive function is back to normal. At that point, other foods can be carefully and gradually reintroduced. Attention should be given to food sensitivities when foods are reintroduced. Processed food products and fast food should stay off the list indefinitely.

Symptoms including abdominal pain, vomiting, severe diarrhea, rectal bleeding, or any other severe intestinal or abdominal complaints should be immediately brought to the attention of a qualified healthcare provider.

Dr. Rawls is a physician who overcame Lyme disease through natural herbal therapy. You can learn more about Lyme disease in Dr. Rawls’ new best selling book, Unlocking Lyme.
You can also learn about Dr. Rawls’ personal journey in overcoming Lyme disease and fibromyalgia in his popular blog post, My Chronic Lyme Journey.

1. G Vighi et al. Allergy and the gastrointestinal system. Clinical & Experimental Immunology. 2008 Sep; 153(Suppl 1): 3-6.