Bloating is one of the most common complaints in the world of digestive health, yet it remains one of the most misunderstood. Many people have resigned themselves to believing that occasional bloating is “normal” — just a minor inconvenience after a big meal or a stressful day. However, in the world of functional medicine, we recognize that bloating is never normal. It is a clear signal from your body that something deeper is going on — typically involving inflammation, gut dysfunction, or microbial imbalance. Left unaddressed, chronic bloating can lead to numerous downstream issues, including nutrient deficiencies, hormonal imbalances, and autoimmune activation.
In this post, we’ll explore the many potential causes of bloating, with a special focus on two of the most overlooked — food sensitivities and Small Intestinal Bacterial Overgrowth (SIBO). Both of these conditions are often missed by the conventional Western medical model but can be identified and treated naturally with the right testing and support.
Common Causes of Bloating
Before diving into the two most overlooked causes, let’s review some of the more commonly recognized reasons why bloating occurs:
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Poor diet: Processed foods, high sugar intake, and artificial additives can irritate the gut and contribute to inflammation.
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Constipation: When stool sits too long in the colon, it can cause excess gas and bloating.
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Stress: Chronic stress affects digestion by altering gut motility and disrupting the gut-brain connection.
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Gut infections: Parasites, yeast overgrowth, and pathogenic bacteria can trigger bloating.
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Hormonal changes: Particularly in women, shifts in estrogen and progesterone can impact gut motility.
While these are all important to consider, two critical causes often fly under the radar: food sensitivities and SIBO.
Food Sensitivities: The Silent Inflammation Triggers
Food sensitivities are not the same as food allergies. While a food allergy can cause immediate and sometimes life-threatening reactions, food sensitivities create a slower, more subtle immune response that can manifest hours or even days after eating the offending food.
Symptoms of food sensitivities can vary widely but often include:
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Bloating
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Gas
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Diarrhea or constipation
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Fatigue
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Brain fog
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Joint pain
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Skin issues like eczema or acne
Common culprits include gluten, dairy, soy, corn, and eggs — but sensitivities can develop to virtually any food. When your immune system reacts to these foods, it causes low-grade inflammation throughout the gut lining. This inflammation disrupts normal digestion, damages the protective mucosal barrier, and leads to increased gas production and water retention — key players in bloating.
The challenge? Food sensitivities are rarely tested for in conventional medical practices unless there is a diagnosis of Celiac disease or a true IgE-mediated allergy. However, functional medicine practitioners use advanced testing like IgG/IgA food sensitivity panels or elimination diets to uncover hidden food triggers.
The good news: Once identified, removing these offending foods can dramatically reduce bloating and allow the gut to heal. Many patients report feeling significantly better within just a few weeks of starting an elimination protocol.
SIBO: The Hidden Cause of Persistent Bloating
Small Intestinal Bacterial Overgrowth (SIBO) is another major — and often missed — cause of chronic bloating. SIBO occurs when bacteria that normally reside in the large intestine migrate up into the small intestine, where they don’t belong.
The small intestine is where the majority of nutrient absorption takes place. When bacteria overgrow in this area, they ferment the carbohydrates you eat, producing hydrogen or methane gas as a byproduct. This excess gas leads to the hallmark symptoms of SIBO:
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Bloating (often worsened after meals)
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Abdominal pain
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Belching
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Diarrhea, constipation, or an alternation between the two
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Nutrient deficiencies (especially B12, iron, and fat-soluble vitamins)
SIBO is vastly underdiagnosed in the Western model, often being mistaken for Irritable Bowel Syndrome (IBS) or simply “stress-related” gut symptoms. However, research now shows that up to 60–70% of IBS cases may actually be rooted in SIBO.
Proper testing is essential to uncover SIBO. A simple, non-invasive breath test that measures hydrogen and methane levels after drinking a sugar solution can accurately detect bacterial overgrowth.
Natural Treatment for SIBO
While conventional medicine often treats SIBO with antibiotics like Rifaximin, these drugs can disrupt the healthy microbiome and fail to address the root cause, leading to frequent relapses. Fortunately, functional medicine offers highly effective, natural alternatives:
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Low FODMAP diet: This diet removes specific types of fermentable carbohydrates that feed the bacterial overgrowth. It can significantly reduce symptoms within days and is a cornerstone of SIBO treatment.
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High-potency herbal antimicrobials: Botanicals such as oregano oil, berberine, neem, and garlic extract have been shown to be just as effective — if not more effective — than antibiotics in clearing SIBO.
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Gut-healing protocols: Supplements like L-glutamine, aloe vera, and probiotics tailored for SIBO can support the repair of the gut lining and restore a healthy microbiome.
Most individuals can experience significant improvement within 30 to 60 days using this natural, multi-pronged approach.
Why Bloating Should Never Be Ignored
It’s tempting to dismiss bloating as a minor inconvenience, especially when it is so common. But remember: common doesn’t mean normal. Chronic bloating is your body’s cry for help. It indicates underlying inflammation, which, if left unchecked, can lead to:
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Increased intestinal permeability (“leaky gut”)
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Immune system dysregulation and autoimmunity
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Hormonal imbalances
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Mood disorders like anxiety and depression
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Nutritional deficiencies
In functional medicine, we aim not just to mask the symptom, but to uncover the root cause and restore true health.
Final Thoughts
If you’re struggling with ongoing bloating, don’t ignore it — and don’t settle for being told it’s “just IBS” or “normal aging.” Through proper testing and a personalized, natural treatment plan, you can uncover hidden food sensitivities, diagnose SIBO, and take concrete steps to heal your gut for good.
Bloating is a messenger — and when you listen to it, you can begin a journey toward deeper wellness, resilience, and vitality.
Ready to get to the root of your bloating? Reach out to our clinic today to learn more about comprehensive functional testing and natural gut healing programs tailored just for you.