The Top 5 Sources of Bloating

bloating gut health intestinal permeability stool test May 23, 2023

Bloating affects millions of people, and it is a signal from our body that something is out of balance in the gut. In my practice, the top 5 sources of gas and bloating are:

1. Food intolerances.

The most common food intolerances are grains (especially gluten), dairy and eggs followed by soy, corn, lectins and nightshades. When we have a healthy, diverse gut microbiome and a balanced immune system these are far less likely to occur. Food intolerances develop when the body has difficulty digesting and fully breaking down certain foods leading to symptoms like gas, bloating, diarrhea, constipation and pain.

A food intolerance, an IgG response, differs from a true food allergy, an IgE response. While signs of a food allergy usually happen right away - rash, swelling, vomiting, anaphylaxis - a food sensitivity reaction can be delayed by up to 72 hours making it really difficult to determine whether the headache you have on Sunday is from the pizza you ate Friday night.

Functional medicine practitioners may use various methods to identify food intolerances, such as an elimination diet or food sensitivity testing. Look for a test that is highly accurate, such as Vibrant Wellness, and then remove the foods causing inflammation while healing the gut lining and reducing inflammation. After 3-6 months, you can then reintroduce them one at a time every 72 hours paying close attention to symptoms.

Remember - the goal is maximum variety so don’t leave those foods out forever because most of the time they’re just collateral damage from intestinal permeability.

2. Low digestive juices.

This includes pancreatic enzymes, bile acid/gallbladder function, and stomach acid/HCl.  The purpose of stomach acid is to break down proteins into individual amino acids (which look like a little string of pearls). It also kills 99.9% of bacteria from getting beyond our gut.

When stomach acid is suppressed due to gut infections such as H.pylori, inflammation, thyroid disease or taking medications such as PPIs, this opens the door for bacterial infections to take hold. It may feel like your food just sits there like a brick, and sometimes lead to reflux, irritating the upper GI and esophagus.

Low stomach acid contributes to gut inflammation, poor nutrient absorption, increased food tolerances and can lead to SIBO (small intestinal bacterial overgrowth). When intestinal permeability is present, it also leads to little pieces of that string of amino acid pearls to leaking through the gut barrier into our bloodstream, where our immune system targets it as a foreign invader and sets off a systemic inflammatory response.

Stomach acid levels can be tested using a Heidelberg test, or you can supplement with HCl or try this Apple Cider Vinegar challenge.

3. Processed protein powders and gums.

Protein powders can be a good addition to increase protein intake, but many contain highly processed ingredients and additives that can be inflammatory to the gut. Anyone with a dairy sensitivity may react to whey protein, the most common type of protein, or egg white protein is another common food sensitivity. Pea protein is a vegan alternative that can cause irritation in those with a damaged mucosal barrier which leads to a lectin sensitivity so you may look for a paleo protein. Inulin is a prebiotic that feeds healthy gut bacteria and it’s found in many powders, supplements, and as a thickening agent however it can feed Candida if yeast or fungal overgrowth is present causing nausea, bloating, diarrhea, constipation, gas and pain.

Gums are typically used as thickeners and emulsifiers, like xanthum gum, guar gum etc. Guar gum comes from the pod of a legume plant and is very commonly used due to its potent thickening power. It can cause bloating, pain and either constipation or act as a laxative leading to diarrhea. It is often also highly sprayed with chemicals.

Xantham gum is made out of refined corn, another product that is known to cause intestinal permeability and digestive issues for many people. It’s generally considered safe, but is found in lots of gluten free products and baked goods and can be reactive for some people. Check things like yogurt, non-dairy milk, protein bars, gluten free products and salad dressings for these gums and thickeners.

4. Not chewing your food well enough.

This is where digestion begins, in the mouth. Amylase is a digestive enzyme in your saliva that is produced by your pancreas and is activated by chewing. It breaks down starch and gets neutralized by your HCl once it reaches the stomach.

How many people chew three times and swallow, or always eat at their desk or on the go? Pick at least one meal a day to sit down at the table, put away your phone, take three deep breaths to put your body into parasympathetic (rest and digest) mode, and chew thoroughly to applesauce consistency. 

Another cause related to this is aerophagia, which means swallowing air when you eat, drink or chew gum.

5. Stress.

This could be physical or emotional stress, your body really can’t tell the difference. Our bodies have their own stress management system called the hypothalamic-pituitary-adrenal (HPA) axis, which is central in managing the gastrointestinal (GI) tract.

Stress shuts down digestion, reduces gastric juices, alters your gut microbiome, lowers the immune system and increases intestinal permeability (‘leaky gut’) but affecting the tight junctions lining your gut wall. This is how stress creates high cortisol and can result in gut dysbiosis, small intestinal bacterial overgrowth (SIBO), pathogenic organisms, opportunistic infections, and intestinal permeability. It also creates high blood sugar, which feeds yeast making you more prone to Candida, small intestinal fungal overgrowth (SIFO) and other yeast or fungus overgrowths.

What else could it be?

Once we rule out SIBO (small intestinal bacterial overgrowth) and thyroid dysfunction, then we may also consider mold exposure, Candida/fungal overgrowth, parasites, uncontrolled autoimmunity and other possible reasons for stubborn non-responsive symptoms.

How To Test

A comprehensive stool test and an intestinal permeability blood test are my favorite tests to address the above issues and really get to the root cause. Once we rule out SIBO and thyroid dysfunction, then you may also consider mold exposure, Candida/fungal overgrowth, parasites, uncontrolled autoimmunity and other possible reasons for stubborn non-responsive symptoms. A comprehensive stool test and an intestinal permeability blood test are my favorite tests to cover all of the above.


To hope, health & happiness, Sara

Function Medicine Clinical Nutritionist, CNS, LDN, FMHC, MS-HNFM



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