SIBO vs Celiac Disease: symptoms, diagnosis, and the critical connection you need to know

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If you've ever struggled with chronic gut issues like bloating, gassiness, diarrhea, or fatigue, you know how life-altering they can be. The daily discomfort, restrictive diets, and constant anxiety about flare-ups can take a toll on both your physical and emotional well-being.

Among the myriad of gut health conditions, SIBO (Small Intestinal Bacterial Overgrowth) and celiac disease often cause confusion due to their overlapping symptoms.

Despite their similarities, these conditions have very different causes, diagnostic criteria, and treatments.

In this blog, I'll break down what SIBO vs Celiac disease is, how to tell them apart, and explore their surprising connection. Plus, I'll share the inspiring story of a client who found answers and relief after years of struggle.

SIBO vs Celiac disease main differences and similarities

What is SIBO?

Let's start with the basics. Small Intestinal Bacterial Overgrowth (SIBO) occurs when bacteria that normally live in other parts of the digestive tract—like the colon—start to overpopulate the small intestine. This imbalance can wreak havoc on your digestive system and lead to a range of debilitating symptoms, including:

  • Persistent bloating and gas
  • Abdominal pain or discomfort
  • Diarrhea, constipation, or alternating between the two
  • Fatigue and brain fog, often caused by nutrient malabsorption
  • Food intolerances, particularly to fermentable carbohydrates (like those found in FODMAP foods)

Living with SIBO can feel like being in an endless cycle of discomfort. You might wake up feeling "off," brace yourself for every meal, and wonder why seemingly healthy foods like cauliflower or garlic leave you doubled over with pain. For many, the restrictive diets they turn to for symptom relief can feel isolating and unsustainable.

But why does SIBO happen in the first place? Causes vary but often include:

  • Impaired gut motility (sometimes due to post-infectious IBS or conditions like diabetes)
  • Structural abnormalities (like adhesions or scar tissue from surgeries or existing conditions like Endometriosis)
  • Usage of certain medications, such as proton pump inhibitors (PPIs), which reduce stomach acid and can disrupt gut bacteria
  • Lack of defense mechanisms in the body to prevent overgrowth (low stomach acid, poor bile flow, immune dysregulation, etc.)

If left untreated, SIBO can lead to long-term nutrient deficiencies, particularly in B12, iron, and fat-soluble vitamins. Thus, early diagnosis and treatment are crucial for improving quality of life.

 

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What is Celiac Disease?

Unlike SIBO, celiac disease is an autoimmune condition.

It's triggered when the immune system mistakenly attacks the lining of the small intestine after consuming gluten—a protein found in wheat, barley, and rye. This immune response damages the intestinal lining (the villi) in your small intestine, leading to inflammation and impaired nutrient absorption.

Common symptoms of celiac disease include:

  • Chronic diarrhea or constipation
  • Abdominal pain and bloating
  • Fatigue and brain fog
  • Unexplained weight loss or difficulty maintaining a healthy weight
  • Signs of malnutrition, such as anemia, brittle nails, or thinning hair

However, not everyone with celiac disease experiences obvious digestive symptoms.

Some people may struggle with "non-classical" symptoms, like joint pain, migraines, depression, or infertility. This wide range of manifestations often makes celiac disease difficult to diagnose, with many individuals going years—if not decades—without answers.

What makes celiac disease particularly challenging is its lifelong nature. Gluten exposure, even in small amounts like just a crumb, can reignite the immune response, which damages the intestinal lining (the villi), impairing the body's ability to absorb nutrients. This requires not just dietary changes but a complete lifestyle shift to avoid cross-contamination in food, cookware, and even cosmetics.

What is gluten?

Gluten is a type of protein found naturally in certain grains, including:

  • Wheat (found in bread, pasta, baked goods)
  • Barley (used in malt products, beer, and soups)
  • Rye (commonly in rye bread and cereals)
  • Triticale (a hybrid of wheat and rye).

Gluten acts as a "glue" that holds food together, giving dough its elasticity and helping it maintain its shape. This is why gluten is so crucial in baking—it gives bread that soft, chewy texture we all recognize.

Beyond obvious foods like bread and pasta, gluten is found in many unsuspecting products, including:

  • Sauces and dressings (soy sauce, gravies)
  • Processed snacks and candy
  • Soups and broths
  • Beer and malt beverages
  • Personal care products (lip balms, shampoos)

Even small amounts of gluten, such as cross-contamination from shared cooking surfaces or utensils, can trigger symptoms in individuals with celiac disease. This is why strict gluten avoidance is necessary for recovery.

For those without celiac disease but with gluten sensitivity (non-celiac gluten sensitivity, NCGS) or other gut issues, gluten can still cause bloating, fatigue, and inflammation. Understanding gluten and its impact is key to managing symptoms and supporting gut health.

Similarities between SIBO and Celiac Disease

It's easy to see why SIBO and celiac disease are often confused.

Both conditions can cause damage to the small intestine or disrupt its functionality. Therefore, both of them share similar symptoms, such as chronic bloating, diarrhea, fatigue, and other discomforts that disrupt daily life.

People with either condition might find themselves misdiagnosed with IBS (irritable bowel syndrome) or dismissed altogether, leaving them frustrated and desperate for answers.

Here's where the overlap happens:

  1. Digestive distress: Both SIBO and celiac disease can lead to bloating, abdominal pain, and irregular bowel movements. These symptoms often worsen after eating, making it difficult to pinpoint specific triggers.
  2. Nutrient deficiencies: Malabsorption is a hallmark of both conditions. In SIBO, bacterial overgrowth can "steal" nutrients from your food before your body has a chance to absorb them. In celiac disease, intestinal damage hinders the absorption of critical nutrients like iron and calcium.
  3. Fatigue and brain fog: Whether caused by nutrient deficiencies or systemic inflammation, both conditions can leave you feeling drained and unfocused, affecting your ability to work, socialize, or even enjoy daily activities.
  4. Emotional impact: Living with unexplained symptoms can feel isolating and stressful. Both conditions are known to take a toll on mental health, with many sufferers experiencing anxiety, depression, or a sense of hopelessness.

However, the similarities end there. While SIBO is fundamentally a bacterial imbalance, celiac disease involves an autoimmune reaction to gluten. This distinction is key to understanding how each condition is diagnosed and treated.

SIBO and Celiac disease symptoms

Key differences between SIBO and Celiac Disease

While SIBO and celiac disease share similar symptoms, their underlying causes and diagnostic approaches are entirely different. Here's a breakdown of the key differences:

Mechanisms:

    • SIBO: A bacterial imbalance caused by an overgrowth of microbes in the small intestine.
    • Celiac disease: An autoimmune condition where the body attacks the small intestine in response to gluten.

Triggers:

    • SIBO: This can be caused by poor gut motility, structural abnormalities, reduced protective mechanisms, or the use of medications. It's often exacerbated by carbohydrate-heavy meals – even on a gluten-free diet, which feed the overgrown bacteria.
    • Celiac disease: Triggered by consuming gluten, which is found in wheat, barley, rye, and certain processed foods. It's also common to have a negative response to dairy and soy due to cross-reactions.

Markers:

    • SIBO: Diagnosed through breath tests or, in rare cases, small intestine aspirates.
    • Celiac disease: Identified via blood tests (tTG-IgA, DGP), intestinal biopsy, and genetic testing. In some cases, a comprehensive stool test can also indicate reactions to gluten (but doesn't equal a diagnostic tool).

Understanding these differences is essential for pinpointing the right diagnosis and creating an effective treatment plan.

Diagnostic criteria and tools

Diagnosing SIBO

The gold standard for diagnosing SIBO is the lactulose or glucose breath test, which measures hydrogen and methane gases produced by bacteria and archaea in the small intestine. (If you live in the USA, the TrioSmart test can also measure hydrogen sulfide gas production.) Elevated levels of these gases after consuming a sugar solution indicate bacterial overgrowth or Intestinal Methanogen Overgrowth (IMO).

However, it's important to be aware that breath tests can sometimes produce false positives or negatives. So, it's important to evaluate symptoms and medical history in conjunction with test results to arrive at the right conclusion.

Diagnosing Celiac Disease

Diagnosing celiac disease requires a multi-step approach:

  1. Blood tests: Screening tests, such as tissue transglutaminase (tTG-IgA) or deamidated gliadin peptide (DGP), are the first step.
  2. Intestinal biopsy: If blood tests are positive, a biopsy of the small intestine confirms the diagnosis by identifying villous atrophy (damage to the gut lining). The patient needs to consume gluten before performing this type of test.
  3. Genetic testing: In ambiguous cases, the HLA-DQ2 and HLA-DQ8 genes are often tested to rule out celiac disease. While these genes are not diagnostic, their absence makes celiac disease very unlikely.

The SIBO-Celiac Disease connection

Did you know that celiac disease can predispose you to SIBO?

Here's how the two conditions are linked:

  • Intestinal damage: In celiac disease, chronic inflammation can damage the small intestine, leading to impaired motility and an environment conducive to bacterial overgrowth.
  • Nutrient deficiencies: A lack of nutrients like zinc and magnesium, often seen in celiac disease, can hinder gut healing and motility.
  • Delayed diagnosis: Undiagnosed or untreated celiac disease increases the risk of developing SIBO due to prolonged intestinal damage.

A 2019 study published in Gut found that individuals with celiac disease are significantly more likely to develop SIBO compared to the general population. This highlights the importance of testing for both conditions if symptoms persist after adopting a gluten-free diet.

SIBO and Celiac disease connection

Treatment for Celiac Disease

The cornerstone of treating celiac disease is a strict lifelong gluten-free diet, which allows the gut lining to heal and inflammation to subside.

Here's a closer look at the process:

  1. Eliminating gluten: Even trace amounts of gluten from cross-contamination can trigger a reaction. This requires diligence when dining out, shopping for groceries, and preparing meals at home.
  2. Healing the gut: Anti-inflammatory foods, bone broth, and supplements like L-glutamine and zinc can support gut repair.
  3. Managing nutrient deficiencies: Many people with celiac disease require supplementation for iron, B12, and fat-soluble vitamins to restore optimal levels.

Holistic approach toward SIBO with Celiac Disease

If you're dealing with SIBO and celiac disease, a one-size-fits-all treatment plan won't work. A functional, holistic approach is key to addressing both conditions simultaneously.

Steps to address SIBO:

  1. Boosting gut motility: Prokinetics, such as ginger or motility agents (natural or pharmaceutical), can prevent bacterial stagnation in the small intestine.
  2. Reducing the overgrowth: Antimicrobial herbs (e.g., berberine, oregano oil) or prescription antibiotics (like rifaximin) may be used to reduce bacterial load.
  3. Supporting the gut microbiome: Managing SIBO doesn't just stop with an elimination protocol. Prebiotics and probiotics tailored to individual needs help restore balance without worsening symptoms.
  4. Dietary adjustments: A low-FODMAP diet is often used temporarily to reduce symptoms while treating the root causes. However, it is also important to incorporate anti-inflammatory nutrients such as omega-3 fatty acids, turmeric, and polyphenol-rich foods, as these can reduce inflammation and support healing.
  5. Lifestyle changes:
    • Stress impacts the gut-brain axis, worsening symptoms. Incorporating stress-relief techniques like mindfulness, yoga, or deep breathing can support healing.
    • Quality sleep promotes gut motility and overall healing. Aim for 7-9 hours per night.
    • Gentle exercise, such as walking, yoga, or Pilates, improves gut motility and reduces stress.
    • Slowing down at meals, chewing thoroughly, and creating a calm eating environment can improve digestion and reduce bloating.
  1. Enzymatic support: Digestive enzymes and bitters can aid nutrient absorption.
  2. Detox pathways: Enhancing liver function with cruciferous vegetables, dandelion tea, or milk thistle can support overall healing.

Addressing both conditions in tandem can improve symptoms, restore balance, and reclaim quality of life.

A case study

When one of my clients first came to me, she was struggling with constant bloating, fatigue, and a restricted diet that felt impossible to manage.

After performing a comprehensive stool test (GI MAP), several red flags were showing up:

  • Inadequate production of digestive enzymes
  • Impaired detoxification
  • Possible signs of intestinal bleeding
  • signs of intestinal inflammation
  • immune system activation and a potential gluten sensitivity
  • Increased risk for an increased intestinal permeability ("leaky gut")

 

Client case Celiac disease

I referred the client to a gastroenterologist for further evaluation, which confirmed a diagnosis of celiac disease. In her case, no SIBO was detected.

From there, we developed a personalized protocol that included:

  • Transitioning to a strict gluten-free diet to avoid triggering immune responses
  • Supporting gut motility to prevent bacterial overgrowth
  • Boosting digestive enzyme production
  • Incorporating anti-inflammatory nutrients and a fiber-rich diet to support the growth of beneficial bacteria, which were also low on her test
  • Supporting the detoxification pathways

Within six months, the client reported feeling more energetic, less bloated, and more in control of her life. As she put it, "Working with Alexandra finally gave me answers to why I was feeling so bloated, tired, irritated, and gassy...She helped me get to the root causes of all my symptoms."

Conclusion

SIBO and celiac disease may look similar on the surface, but their causes, diagnostic criteria, and treatments are entirely different. Understanding these differences—and their potential connection—can help you get the right diagnosis and embark on a path to healing.

If you're struggling with persistent gut issues, don't settle for temporary solutions. A holistic approach that addresses the root causes of your symptoms can help you reclaim your life. Remember, with the right tools, support, and mindset, healing is within reach!

This post is only for informational purposes and is not meant to diagnose, treat, or cure any disease. I recommend always consulting your healthcare practitioner before trying any treatment or dietary changes.

References
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SIBO-related sources:

  • Dukowicz, A. C., Lacy, B. E., & Levine, G. M. (2007). Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterology & hepatology, 3(2), 112–122.
  • Cho, Y. K., Lee, J., & Paik, C. N. (2023). Prevalence, risk factors, and treatment of small intestinal bacterial overgrowth in children. Clinical and experimental pediatrics, 66(9), 377–383. https://doi.org/10.3345/cep.2022.00969
  • Khoshini, R., Dai, SC., Lezcano, S. et al.A Systematic Review of Diagnostic Tests for Small Intestinal Bacterial Overgrowth. Dig Dis Sci 53, 1443–1454 (2008). https://doi.org/10.1007/s10620-007-0065-1
  • Sharabi, E., Rezaie, A. Small Intestinal Bacterial Overgrowth. Curr Infect Dis Rep26, 227–233 (2024). https://doi.org/10.1007/s11908-024-00847-7
  • Ghoshal UC, Shukla R, Ghoshal U.  Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome: A Bridge between Functional Organic Dichotomy.  Gut and Liver 2017;11:196-208.  https://doi.org/10.5009/gnl16126
  • Lim, J., & Rezaie, A. (2023). Pros and Cons of Breath Testing for Small Intestinal Bacterial Overgrowth and Intestinal Methanogen Overgrowth. Gastroenterology & hepatology, 19(3), 140–146.
  • Rezaie, Ali MD, MSc, FRCP(C)1; Buresi, Michelle MD2; Lembo, Anthony MD3; Lin, Henry MD4; McCallum, Richard MD5; Rao, Satish MD6; Schmulson, Max MD7; Valdovinos, Miguel MD8; Zakko, Salam MD9; Pimentel, Mark MD, FRCP(C)1 on behalf of The North American Consensus group on hydrogen and methane-based breath testing. Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders: The North American Consensus. American Journal of Gastroenterology 112(5):p 775-784, May 2017. | DOI: 10.1038/ajg.2017.46

 

Celiac disease-related sources:

  • Parzanese, I., Qehajaj, D., Patrinicola, F., Aralica, M., Chiriva-Internati, M., Stifter, S., Elli, L., & Grizzi, F. (2017). Celiac disease: From pathophysiology to treatment. World journal of gastrointestinal pathophysiology, 8(2), 27–38. https://doi.org/10.4291/wjgp.v8.i2.27
  • Caio, G., Volta, U., Sapone, A. et al.Celiac disease: a comprehensive current review. BMC Med 17, 142 (2019). https://doi.org/10.1186/s12916-019-1380-z
  • Lebwohl, B., Sanders, D. S., & Green, P. H. R. (2018). Coeliac disease. Lancet (London, England), 391(10115), 70–81. https://doi.org/10.1016/S0140-6736(17)31796-8
  • Parzanese, I., Qehajaj, D., Patrinicola, F., Aralica, M., Chiriva-Internati, M., Stifter, S., Elli, L., & Grizzi, F. (2017). Celiac disease: From pathophysiology to treatment. World journal of gastrointestinal pathophysiology, 8(2), 27–38. https://doi.org/10.4291/wjgp.v8.i2.27
  • Niland, B., & Cash, B. D. (2018). Health Benefits and Adverse Effects of a Gluten-Free Diet in Non-Celiac Disease Patients. Gastroenterology & hepatology, 14(2), 82–91.
  • Barbaro, M. R., Cremon, C., Stanghellini, V., & Barbara, G. (2018). Recent advances in understanding non-celiac gluten sensitivity. F1000Research, 7, F1000 Faculty Rev-1631. https://doi.org/10.12688/f1000research.15849.1

 

SIBO-Celiac disease relationship-related sources:

  • Losurdo, G., Marra, A., Shahini, E., Girardi, B., Giorgio, F., Amoruso, A., Pisani, A., Piscitelli, D., Barone, M., Principi, M., Di Leo, A., & Ierardi, E. (2017). Small intestinal bacterial overgrowth and celiac disease: A systematic review with pooled-data analysis. Neurogastroenterology and motility, 29(6), 10.1111/nmo.13028. https://doi.org/10.1111/nmo.13028
  • Shah, A., Thite, P., Hansen, T., Kendall, B. J., Sanders, D. S., Morrison, M., Jones, M. P., & Holtmann, G. (2022). Links between celiac disease and small intestinal bacterial overgrowth: A systematic review and meta-analysis. Journal of Gastroenterology and Hepatology, 37(12), 2311–2321. https://doi.org/10.1111/jgh.15920
  • Evans KE, Higham S, Smythe A, et al Small bowel bacterial overgrowth in coeliac disease: a cause of presenting symptoms?.Gut 2011;60:A83-A84. https://gut.bmj.com/content/60/Suppl_1/A83.2
  • Sroka, N., Rydzewska-Rosołowska, A., Kakareko, K., Rosołowski, M., Głowińska, I., & Hryszko, T. (2023). Show Me What You Have Inside—The Complex Interplay between SIBO and Multiple Medical Conditions—A Systematic Review. Nutrients, 15(1), 90. https://doi.org/10.3390/nu15010090
  • Patel, Akash & Vaghani, Utsav & Mehta, Sarang & Sri, Shivaramakrishna. (2023). Celiac Disease and Upper Gastrointestinal Microbiota Disorders: A Meta-Analysis Investigating Small Intestinal Bacterial Overgrowth (SIBO) and H. pylori. 2. 1-11. 10.5281/zenodo.10066586.
  • Catassi, C., Alaedini, A., Bojarski, C., Bonaz, B., Bouma, G., Carroccio, A., Castillejo, G., De Magistris, L., Dieterich, W., Di Liberto, D., Elli, L., Fasano, A., Hadjivassiliou, M., Kurien, M., Lionetti, E., Mulder, C. J., Rostami, K., Sapone, A., Scherf, K., Schuppan, D., … Sanders, D. S. (2017). The Overlapping Area of Non-Celiac Gluten Sensitivity (NCGS) and Wheat-Sensitive Irritable Bowel Syndrome (IBS): An Update. Nutrients, 9(11), 1268. https://doi.org/10.3390/nu9111268
  • Charlesworth, R. P. G., & Winter, G. (2020). Small intestinal bacterial overgrowth and Celiac disease – coincidence or causation? Expert Review of Gastroenterology & Hepatology, 14(5), 305–306. https://doi.org/10.1080/17474124.2020.1757428

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