A Functional Nutrition Approach to Fibromyalgia, Focusing on Dysbiosis & SIBO

Fibromyalgia is a disorder characterized by widespread pain and tenderness in the muscles and bones, accompanied by fatigue, sleep, memory and mood issues. Fibromyalgia is most common in women, though it can occur in men. It most often starts in middle adulthood but can occur in the teen years and in old age.

Causes of Fibromyalgia

Conventional doctors are taught the cause of fibromyalgia is a mystery but suspect it may be genetic or caused by abnormal pain signaling – the nervous system not processing pain signals in the usual way. However, Dr. Alex Vasquez, a renown functional medicine doctor, would say otherwise. He says research shows gut dysbiosis accounts for all the problems seen in fibromyalgia. He also says people with fibromyalgia have mitochondrial dysfunction, neuroinflammation, and pain – all which link to and stem from gut dysbiosis.

Dr. Alex Vasquez’s Pathophysiological Components of Fibromyalgia:

  1. Dysbiosis (gut bacterial overgrowth aka: leaky gut and a high prevalence of SIBO)
  2. Mitochondrial dysfunction (often caused by SIBO)
  3. Neuroinflammation and Central Sensitization (often caused by SIBO)

Fibromyalgia's Link To Gut Dysbiosis and SIBO

Your GI tract is full of trillions of harmless microbes – bacteria, fungi, viruses, and even parasites – all living together in balance. When there’s any interruption in the balance of gut microbes, it can lead to dysbiosis. The body is usually able to correct the imbalance without treatment, but if symptoms become more serious, other solutions must be implemented.

One cause of dysbiosis is when microbes settle in the wrong place and cause problems, which is called Small Intestinal Bacterial Overgrowth (SIBO). Problems occur when normal bacteria and flora of the large intestine shifts upward and starts taking up residence in the small intestine.

People with fibromyalgia have a high prevalence of SIBO, which often leads to increased intestinal permeability (aka: leaky gut). When the intestinal lining is working properly, it forms a tight barrier that controls what gets absorbed into the bloodstream. When the gut lining is damaged, small gaps in the intestinal wall called tight junctions allow undigested or partially digested food particles, toxins, and bacteria to “leak” through the intestinal wall and enter the bloodstream. This triggers inflammation and changes in the gut bacteria, which may play a role in the development fibromyalgia.

Research shows there’s a relationship between the severity of the gut bacteria overgrowth and the severity of fibromyalgia symptom manifestation. When one thing is bad, the other is bad too, but which came first? Most likely…the dysbiosis came first. Fibromyalgia patients respond to antibiotics for treating SIBO, which means the antibiotics are killing off something in the gut and the person is therefore getting a positive response from it. However, rather than turning to antibiotics, there are a variety of botanicals and herbs that can be used, instead of antibiotics, to kill off bacteria and move it out of the bowel.

Treat the disease by treating the cause of the problem. Most evidence points toward dysbiosis, mainly in the gut, and particularly SIBO. Therefore, someone with fibromyalgia must target SIBO, and along with that, target overall health.

What Causes Dysbiosis and SIBO?

A variety of things cause dysbiosis and maintain the SIBO:

  • Chronic stress
  • Eating too many fermentable carbohydrates in the diet (ie: wheat, potatoes)
  • Eating foods with glyphosate, a pesticide, which basically acts as an antibiotic and kills good gut bacteria, which promotes gut dysbiosis.
  • Immune impairment, in general.
  • The standard American diet, which is low in fiber and high in sugar and saturated fats
  • Heavy alcohol use disrupts gut balance

Signs You Have SIBO

If you have air in your gut, it’s because the bacteria are producing it, so gas & bloating after eating are basically a diagnosis for SIBO or IBS.

If someone has diarrhea, it’s because certain bacteria are producing excess hydrogen, which promotes a laxative effect. If a patient has constipation, it’s because hydrogen sulfide and methane are paralytic agents on the gut (slow motility down).

5-Part Nutrition Protocol for Gut Dysbiosis and SIBO

1. Paleo-Mediterranean Diet (low-carb): fruits, vegetables, nuts, seeds, barriers, high-quality protein; avoid allergen foods. A low-carb version is important because you want to starve the bacteria in the gut, which thrive on carbohydrates. Adequate protein is important too – are you getting enough? Here’s how to calculate your protein requirements.   

2. Multivitamin/multimineral, high-potency supplement.

3. Vitamin D3: 2,000-4,000-10,000 IU/d to optimize serum levels

4. Combination fatty acid therapy: ALA, GLA, EPA, DHA, Oleic acid; these are taken specifically for neuroinflammation and to support the gut microbiome.

5. Probiotics: especially with allergies, IBS and/or antibiotics

6. Exercise

7. Sleep/rest/relaxation

Protocol to Target the SIBO

How do we specifically target the SIBO? Clean up the gut by changing the diet, supporting the immune system, and promoting peristalsis with laxatives (magnesium, vitamin C). You don’t want fermentable carbs in the diets of people who already have overgrowth. Eat plenty of seeds because they aren’t fermentable. 

1. A diverse, plant-based diet with non-fermentable fibers and seeds.

2. You must go #2 every day. If this isn’t happening, consider laxatives. You want loose stools. You don’t want to be constipated!

3. Typical magnesium dose: 600 mg/day; some people need more, some need less. Base it off loose stools, which indicates you’ve met your threshold.

4. Vitamin C: 2 grams 3 times per day for a total of 6 grams

5. Probiotics

6. Support the Immune System (Vitamin D, Vitamin A, Zinc)

7. Stress avoidance and stress management

8. Use of antimicrobials (2)

          *Berberine: 500 mg 2-3x/day, for about 3 months

          *Emulsified and time-released oregano oil up to 600 mg/d in divided doses

          *Rifaximin, other natural and gut-specific antimicrobials

Magnesium Dosage

If the person has magnesium deficiency (ie: muscle cramps, grinding teeth, constipation, sugar cravings), you can dose magnesium until symptoms go away. The limited effect is GI distress, particularly diarrhea, and people respond differently to different forms. If a person is reacting to a low magnesium dose, such as 120 mg/day, that isn’t the problem of the magnesium – it’s likely nutrient intolerance in the gut because there’s gut dysbiosis or SIBO.

In conclusion, you have to restore immune function, clean up the diet and increase gut motility.

Kelly Harrington, MS, RDN

Registered Dietitian Nutritionist for Healthy Goods


1. Dr. Alex Vasquez, InflammationMastery.com

2. Dr. Alex Vasquez. Revisiting the five-part nutritional wellness protocol: the supplemented paleo-mediterranean diet. Nutritional Wellness. 2005 Sept.

3. Ann Rheum Dis 2004.

4. Rheumatology 2008.

5. Junling Han et al. Modulating gut microbiota as an anti-diabetic mechanism of berberine. MedSciMonit.

6. Force M et al. Inhibition of enteric parasites by emulsified oil of oregano in vivo. Phytotherapy Research.

7. Wallace DJ, Hallegua DS. Fibromyalgia: the gastrointestinal link. Curr Pain Headache Rep. 2004 Oct;8(5):364-8

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