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Could SIBO Be The Cause Of Your Headaches?

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Could SIBO Be The Cause Of Your Headaches?

In the realm of gastrointestinal disorders, SIBO has gained attention for its associations with irritable bowel syndrome and the wide range of symptoms it can cause. Speaking to the complex interplay between gut and neurological health, SIBO and headaches often co-occur. This article delves into the fascinating connection between SIBO and headaches, shedding light on the possible mechanisms linking these seemingly disparate conditions and offering insights into their management and treatment.


What Is SIBO?

SIBO stands for small intestinal bacterial overgrowth. It is a medical condition characterized by an abnormal increase in the number and/or types of bacteria in the small intestine. Normally, the small intestine has a relatively low population of bacteria compared to the colon. However, in SIBO, bacteria from the colon or other parts of the digestive tract migrate and overgrow in the small intestine. 

This overgrowth of bacteria in the small intestine can lead to various gastrointestinal symptoms, including abdominal pain, bloating, diarrhea, constipation, and excessive gas production. SIBO can interfere with the normal digestion and absorption of nutrients, as the bacteria may consume nutrients intended for the host, leading to nutrient deficiencies.

The exact cause of SIBO can vary but is often related to issues with the normal functioning of the gastrointestinal tract, such as impaired motility (the movement of food and waste through the digestive system), structural abnormalities, or certain medical conditions. Risk factors for SIBO include prior gastrointestinal surgeries, conditions like irritable bowel syndrome (IBS), and the use of certain medications that affect gut motility. Treatment usually involves prescription or natural antibiotics to reduce bacterial overgrowth and dietary changes to manage symptoms and prevent recurrence. In some cases, underlying conditions contributing to SIBO may also need to be addressed. (7

What Are Headaches?

Headaches are a common medical condition characterized by pain or discomfort in the head or upper neck region. They can vary in intensity, duration, and location, and they may be accompanied by other symptoms such as nausea, sensitivity to light (photophobia), and sensitivity to sound (phonophobia). Headaches can significantly impact a person's daily life and well-being.

Primary Headaches

Primary headaches are not caused by an underlying medical condition and are often the result of overactivity or problems with the pain-sensitive structures in the head. The exact cause of primary headaches is not fully understood and may involve a combination of genetic, environmental, and neurological factors. Triggers for primary headaches can include stress, hormonal changes, certain foods, lack of sleep, and environmental factors. (14

Common types of primary headaches include (14, 21): 

  • Tension-type headaches: These are the most common type of headache and are often described as a dull, constant ache that can affect both sides of the head.
  • Migraines: Migraine headaches are typically characterized by severe, throbbing pain, often on one side of the head, and are often accompanied by other symptoms like nausea, vomiting, and sensitivity to light and sound.
  • Cluster headaches: These are excruciating headaches that tend to occur in clusters, often at the same time of day or night. They are typically one-sided and may be associated with eye symptoms like redness and tearing.

Secondary Headaches 

Secondary headaches are caused by an underlying medical condition or other factors. Possible causes of secondary headaches include (14):

What Is the Connection Between SIBO and Headaches?

Along with the digestive symptoms discussed above, patients with SIBO or other gastrointestinal conditions may also suffer from headaches. For example, research suggests that migraine patients are more likely to have irritable bowel syndrome, and patients with non-celiac gluten sensitivity commonly experience headaches (18, 26). 

While the connection between SIBO and headaches is not well-established or fully understood, there are potential links between the two conditions. When you understand the relationship between gut health, dysbiosis, the immune system, inflammation, and nutrient absorption, it's easier to comprehend how SIBO can manifest with headaches as a symptom. 

The gut-brain axis is a complex network of communication pathways that involves the nervous, endocrine, and immune systems. It allows the gut and the brain to influence each other's functions. The gut is home to a vast community of microorganisms (the gut microbiota) that play a crucial role in various aspects of health, including the regulation of the gut-brain axis. SIBO disrupts the healthy microbiome; this dysbiosis may lead to nutrient malabsorption and a disruption in normal immune signaling, neurotransmitter synthesis, and hormone production. Collectively, these imbalances can negatively influence neurological function and promote inflammation, leading to increased frequency of headaches.  

Additionally, SIBO is associated with increased intestinal permeability, also called "leaky gut." Leaky gut is a condition in which the small intestine's lining becomes excessively porous, allowing substances like bacteria, toxins, and undigested food particles to pass through the intestinal barrier and enter the bloodstream. Exposure to undigested food particles that enter the bloodstream activates an immune response, triggering inflammation and antibody production systemically (22). Substantial evidence strongly suggests IgG-mediated food sensitivities as one of the dietary-related triggers for migraine headaches.

Functional Medicine Lab Tests to Test for SIBO and the Health of the Gut-Brain Axis

Functional medicine lab tests are crucial in diagnosing SIBO and evaluating the intricate relationship between gut health and the brain through the gut-brain axis. Here are tests that may help determine whether poor gut health contributes to your headaches.

SIBO Breath Testing

In place of an endoscopic aspirate and fluid culture of the small intestine, which is invasive and expensive, SIBO breath testing is the preferred clinical method for diagnosing SIBO. The breath test is a noninvasive test performed at home to measure the amount of hydrogen or methane you exhale after drinking a mixture of glucose or lactulose and water. A rapid rise in either or both gas levels is diagnostic for SIBO. (4)

Comprehensive Stool Analysis

A comprehensive stool analysis can provide valuable insights into the gut-brain axis by examining various factors related to gastrointestinal health, inflammation, and gut microbiota composition. 

Micronutrient Testing

Generally speaking, micronutrients play critical roles in various physiological processes, including brain function, gut health, and controlling inflammation. Deficiencies in iron and vitamins A, B12, and D are common in patients with SIBO (5). A micronutrient test offers valuable insight into the gut and neurological health by assessing the levels of essential vitamins, minerals, antioxidants, fatty acids, and amino acids in the body. 

Neurotransmitter Testing

Our commensal gut bacteria and the brain produce and respond to the same signaling chemicals called neurotransmitters, including GABA, serotonin, norepinephrine, dopamine, and acetylcholine. Imbalances in any or all of these can contribute to gastrointestinal dysfunction, neuroinflammation, and changes in mood and cognition. By assessing neurotransmitter levels, this test can provide insights into how the gut and the brain communicate, potentially revealing imbalances or disruptions in neurotransmitter signaling that may contribute to gut-related and neurological symptoms. (19


Integrative Approach to Treating SIBO and Headaches

An integrative approach to treating SIBO and headaches combines conventional medical interventions with complementary therapies, dietary modifications, and lifestyle changes to address the conditions holistically.

Nutritional Recommendations

Elimination diets are a mainstay in treating both SIBO and headaches. Elimination diets should be customized based on the patient's specific dietary triggers, which can be identified using diet diaries and laboratory testing.

Elimination diets don't necessarily treat SIBO, but they reduce bacterial food sources to provide symptom palliation while the overgrowth is being addressed. Fermentable carbohydrates, called FODMAPs, commonly exacerbate SIBO symptoms. These carbohydrates ferment in the gut, leading to the production of gas, causing SIBO symptoms. The low-FODMAP diet restricts the intake of FODMAPS to prevent excessive gas production and relieve digestive symptoms. (6

Patients should also avoid identified trigger foods for headaches, commonly including caffeine, MSG, cocoa, aspartame, cheese, citrus, and nitrates. Other helpful diets for treating headaches include the ketogenic, low-histamine, gluten-free, and folate-rich diets. (21

Helpful Supplements

Treating SIBO involves eradicating the bacterial overgrowth with an antimicrobial agent. For patients who prefer avoiding antibiotic use, herbal antimicrobials have been proven to be just as effective in treating SIBO. Common botanical supplements for treating SIBO include oregano, berberine, neem, and allicin. (5

Other gut-supportive supplements can be used in a holistic treatment protocol to heal the gut, support digestion, and promote a healthy microbiome. Digestive enzymes help digest food particles to their small building blocks; this can reduce dietary-mediated intestinal inflammation and meal-related digestive symptoms and improve food tolerance. L-glutamine is the preferred fuel source for the cells lining the small intestine. Given its ability to assist in cellular repair processes and preserve epithelial tight junctions, it is a popular supplement recommended by functional medicine doctors to heal leaky gut. Finally, supplemental probiotics and prebiotics modulate the gut microbiome to positively impact the gut-brain axis (2). 

Complementary and Integrative Approaches

Stress is known to contribute to impaired gastrointestinal motility and trigger headaches. Complementary and integrative modalities, such as biofeedback, acupuncture, and massage, have produced positive results in treating stress disorders, IBS, and headaches. 



While the emerging link between SIBO and headaches needs to be further explored, it underscores the intricate relationship between the gut and the brain. Addressing SIBO's impact on neurological health represents an opportunity for symptom relief and a step toward a more comprehensive understanding of the interconnectedness of our bodily systems.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
Learn More

Lab Tests in This Article

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2. Ansari, F., Neshat, M., Pourjafar, H., et al. (2023). The role of probiotics and prebiotics in modulating of the gut-brain axis. Frontiers in Nutrition, 10.

3. Chedid, V., Dhalla, S., Clarke, J. O., et al. (2014). Herbal Therapy is Equivalent to Rifaximin for the Treatment of Small Intestinal Bacterial Overgrowth. Global Advances in Health and Medicine, 3(3), 16–24.

4. Cloyd, J. (2023, March 14). SIBO Testing 101: A Complete Guide to The Top 3 SIBO Tests. Rupa Health.

5. Cloyd, J. (2023, March 30). An In-Depth Overview of the Three Types of SIBO: Hydrogen, Methane, Hydrogen Sulfide. Rupa Health.

6. Cloyd, J. (2023, April 26). Dietary Modifications for a Successful SIBO Treatment Plan. Rupa Health.

7. Cloyd, J. (2023, May 4). A Functional Medicine SIBO Protocol: Testing and Treatment. Rupa Health.

8. Cloyd, J. (2023, May 24). What are Digestive Enzymes: How to Test Your Patients Levels. Rupa Health.

9. Cloyd, J. (2023, June 19). A Functional Medicine Post Stroke Protocol: Testing, Therapeutic Diet, and Integrative Therapy Options. Rupa Health.

10. Cloyd, J. (2023, July 21). A Functional Medicine Migraine Protocol: Comprehensive Testing, Nutritional Considerations, and Supplements. Rupa Health.

11. Conner, V. (2022, August 26). 9 Remedies For Ear Infection Pain Backed By Science. Rupa Health.

12. Greenan, S. (2021, November 2). Constant Burping Is A Sign Of This Harmful Bacterial Overgrowth. Rupa Health.

13. Greenan, S. (2021, November 18). How To Do A Low FODMAP Elimination Diet. Rupa Health.

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16. Khakham, C. (2023, June 14). How To Start Using Biofeedback in Your Wellness Clinic. Rupa Health.

17. Krishna Rao, R. (2012). Role of Glutamine in Protection of Intestinal Epithelial Tight Junctions. Journal of Epithelial Biology and Pharmacology, 5(1), 47–54.

18. Li, C., Yu, S., Li, H., et al. (2017). Clinical features and risk factors for irritable bowel syndrome in Migraine patients. Pakistan Journal of Medical Sciences, 33(3), 720–725.

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21. Neibling, K. (2023, February 27). Integrative Medicine Treatment for Headaches. Rupa Health.

22. Orbeta, R. (2022, May 9). Is Your Child Suffering From A Food Sensitivity? Rupa Health.

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27. Yoshimura, H. (2023, March 3). A Functional Medicine Approach to Sinusitis. Rupa Health.

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