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SIBO and Migraines

Written and verified by Holly Hazen

SIBO And Migraines @migrainesavvyWhat To Do If You Have SIBO And Migraines

SIBO stands for small intestine bacterial overgrowth. To put it simply, it's having a bacterial overgrowth of many different types of bacteria that belong in the large intestine backed up in the small intestine. And when bacteria are in the wrong place, it can wreak havoc with your health.

We all have bacteria in our small intestine, which is the place where you digest your food, but we have an infinitely higher number of bacteria in the colon (the large intestine). [4]

The fermentation of non-soluble sugars by intestinal flora is a normal function of the colon. However, it is not a normal function of the small intestine. When abnormal fermentation takes place in the small intestine, it can lead to fatigue, malaise, irritable bowel, bladder function disorders, depression, pulmonary problems and headaches. More problematically, it can lead to dysbiosis (microbial imbalance). [3]

Let me tell you how SIBO and migraines are linked, and what you can do help reduce both.

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SIBO and Migraines - What You'll Learn In This Article:

  • SIBO and migraines. Are they linked?
  • Can SIBO cause migraines? Can it trigger a migraine attack?
  • How would I know if I have SIBO?
  • What causes SIBO?
  • Is there a test for SIBO?
  • Are there medications I can take for SIBO?
  • Recommended Treatments
  • 6 Natural Things That Help SIBO and Migraines
  • SIBO Friendly Chicken Soup Recipe
  • SIBO and Migraines - 5 More Tips

SIBO and migraines. Are they linked?

I'm going to talk about constipation a bit later. But a lot of the migraine medications you may be prescribed will have constipation as a side effect. This is a problem, as it can cause the back up of bacteria up into your small intestine. And constipation = SIBO. More specifically...

Constipation = SIBO (C)

Diarrhea = SIBO (D)

We have good (and bad) bacteria, and it should be lower down in your digestive tract in the large intestine. Bacterial overgrowth further up the intestines can cause many issues. It's also associated with reflux and H pylori infection. "H. pylori and SIBO are related to elevated histamine levels in the blood. Histamine and other molecules like it are vasoactive, in that they can cause changes in the dilation of blood vessels. The dilation of the blood vessels is thought to be one of the mechanisms of migraine and the triptans many people take for episodic migraine contract blood vessels, thereby, hopefully stopping the migraine." [1]

What we often see is a link between migraine or indeed other neurological issues like anxiety and bacterial imbalance in the gut. H. pylori infection is one of these, as is Small Intestinal Bacterial Overgrowth (SIBO). 

~ Dr. Ciara Wright [1]

Aside from good and bad bacteria that are created in the gut, are also some essential hormones and neurotransmitters that have a significant effect on our brains. "Some studies have also shown that a disruption to the normal, healthy balance of bacteria in the microbiome can cause the immune system to overreact and contribute to inflammation of the GI tract, which in turn can lead to the development of diseases that occur not only throughout your body, but also in your brain." [1]

A study by Eaton et. al, (2004 in Great Britain) found that patients with abnormal gut fermentation had resulting vitamin B, zinc, and magnesium deficiencies. They also have an intolerance to alcohol, and typically crave carbohydrates and sweets, usually chocolates, cookies and bread. "These foods, according to the study, are often consumed in a ‘binge’, followed by a brief period of abstention.” [3]

All of those findings ring migraine alarm bells. Magnesium is a well known deficiency found in people living with migraine. And we all know about those cravings.

My #1 Choice in Magnesium Supplements

Can SIBO cause migraines?

I think that SIBO and migraines are linked. And I think that SIBO can trigger migraine attacks. Although no studies have been done on these two combined, there are studies that have been done with other gut issues. 

Currently, sufficient evidence exists linking the increased frequency of several GI disorders with migraine compared to the general population. The gut-brain axis plays an important role in the association between GI disorders and migraine.

~ Cámara-Lemarroy, Carlos R et al. [5]

Dr. Susanne Booth is a Naturopathic Doctor and Physical Therapist at Sojourns Community Health Clinic - she has found that SIBO symptoms can cause headaches.

"The symptoms of SIBO include bloating or abdominal gas, abdominal pain and cramps, constipation or diarrhea or an alternation between the two, heartburn, nausea, malabsorption and systemic inflammation that may cause headaches, joint pain and fatigue." [2]

Constipation alone, in my opinion, can trigger migraine attacks. And diarrhea can cause dehydration, a well known migraine trigger.

Also, SIBO significantly impacts your digestion of food and absorption of nutrients (because it damages the gut lining) which is problematic for us as people living with migraine - having slow stomach motility (gastroparesis) to start with. [4]

SIBO and migraines work against each other. I think having SIBO can cause an attack and I think having migraines predisposes us to SIBO.

How would I know if I have SIBO?

Here are some common symptoms you might experience:

  • Constant, excessive bloating and or burping within one hour after eating
  • Abdominal pain and cramps
  • Constipation or diarrhea or an alternation between the two
  • Long-standing, stubborn constipation
  • Impaired digestion (excessive fullness after eating, stomach pain or cramping, undigested food in your stool, greasy stools that are difficult to flush)
  • Headaches, joint pain and fatigue
  • Exhaustion (from being undernourished and not digesting your food properly)
  • Heartburn or acid reflux
  • Numerous food sensitivities
  • Brain fog
  • Nausea
  • Depression and anxiety (the gut, the brain & the nervous system are a team)
  • Trouble digesting most carbohydrates (FODMAPS diet would ease symptoms)
  • Vitamin A or Vitamin D deficiency [4]

I did this SIBO Recovery Roadmap™ Course - it was fantastic.

SIBO Recovery Roadmap™ CourseSIBO Recovery Roadmap™ Course

What causes SIBO?

There can be one or many causes of SIBO for you. One of the most common causes of SIBO is antibiotic treatment.

Our intestinal bacteria live in symbiotic relationships with each another. "Once several strains of beneficial flora have been selectively removed, others may proliferate unchecked." [3]

Slow motility or impaired motility (Migrating Motor Complex) can cause SIBO. 

Steady peristalsis of the small intestine normally flushes any excess bacteria out into the large intestine, where it can be effectively neutralized. But when peristalsis is slowed or impaired, the bacteria have a greater chance to multiply. And, although the ileocecal valve is designed to prevent a "backwash of bacteria from the large intestine, some of the billions of bacteria per milliliter found in the colon may invade the small intestine." [3]

Another major contributory factor in the development of SIBO is from the use of antacids which can cause low stomach acid - hypochloridria.

Low stomach acid permits the passage of bacteria which may have otherwise been destroyed in the stomach. And it reduces the "secretion of pancreatic enzymes which are, in part, stimulated by the acid chyme passing into the duodenum. Once digestion is impaired by a reduction in enzymes, there is additional substrate for bacterial overgrowth." [3]

Stress can be another cause of both SIBO and migraines. 

When your body is under stress you produce more cortisol (also called adrenaline). This is an important function of the body! The increased cortisol gives you the ability to stand and fight or run away quickly from the stressor. And it also reduces stomach acid production if you need to fight or flee the scene. 

Then it gets complicated. When you have less stomach acid, the pH of your stomach goes up from its normal pH of about 2. “The increased pH when we are stressed may allow bacteria to survive and get through to the small intestine, bacteria that would normally be killed off in the lower pH. These bacteria set up shop and stay in the small intestine wreaking havoc.” [2]

Here are a few other things that can cause SIBO:

  • Chronic infections and antibiotic use (sometimes even just 2 or 3 rounds of antibiotics) 
  • Stealth infections like: chronic fatigue syndrome, fibromyalgia, chronic viral illness, Lyme disease (tick bite)
  • Inadequate or low stomach acid
  • Overconsumption of alcohol, sugar, birth control pills, or NSAIDs (anti-inflammatories)
  • Digestive diseases like Celiac, Crohn’s, ulcerative colitis
  • Irritable bowel syndrome
  • Mold toxicity
  • Food poisoning
  • Thyroid disorder
  • Traumatic Brain Injury
  • Impaired motility (Migrating Motor Complex)
  • An autoimmune condition
  • Diabetes (metabolic syndrome, pre-diabetes) 
  • Injured, lazy, or flimsy ileocecal valve [4]

Is there a test for SIBO?

Yes. It's a simple, non-invasive breath test you can do at home. The test is called the Lactulose Breath Test (also known as the Hydrogen Breath Test).

The breath test measures the amount of hydrogen and methane (two gases which are only produced by bacteria) after the ingestion of lactulose, a non-digestible sugar used to treat mild constipation. [3]

It's best to work with whoever your doctor or specialist recommends. Here in Australia The SIBO Doctor links to the tests, and in the USA Dr. Siebecker's website links to the best tests. The links are below.

Are there medications I can take for SIBO?

Yes. There are some very effective medications and herbal treatments for SIBO. 

I suggest you work with a specialist as SIBO can be really hard to treat. SIBO and migraines makes it more complicated but from my own personal experience the SIBO medications did not interreact with my migraine medications.

As I always say - best to work with your doctor on this and a SIBO specialist.

Here are the best website resources I have found to date:

Dr. Allison Siebecker's preferred antibiotics to use are Rifaximin (Xifaxan) and Neomycin. "They are almost completely non-absorbable which means they stay in the intestines, having a local action and don't cause systemic side effects, such as urinary tract infections. They are chosen specifically for this property which allows them to act only where they are needed.  Metronidazole, a systemic antibiotic, is also used."

Generally, antibiotic treatments are given for 10 – 30 days (depending on your test results) until the overgrowth  has cleared. And you may need to do a few rounds before it is completed eliminated.

I chose to go the pharmaceutical medication route as it was faster. The herbal treatments can take 3 months or longer to take hold. It's a personal preference. 

I've done 5 more rounds of Rifaximin and Neomycin this year to treat my chronic SIBO. I decided to do the SIBO SOS course - it was well worth the money. I saw 3 doctors who all seemed to miss a few things! And I felt more in control after doing the course. SIBO and migraines is tricky.

After a second relapse, I was told by my doctor to combine two prokinetic's – Iberogast after food 3 times a day, and prucalopride before bed.

Sometimes it takes a few different things and combinations to work.

Recommended Treatments

Treatments for SIBO are varied. One option is to use prescription antibiotics like Rifaximin which is targeted and non-systematic – safe to use. 

Antimicrobial herbs are another option that do not disrupt the large intestinal bacteria. Diet changes and using certain types of probiotics are other options.

The most important thing is to stop the bacteria from backing up into the small intestine in the first place. 


The second line of treatment, often given simultaneously and/or immediately after treatment with antibiotics, is probiotics. In milder cases of SIBO, antibiotics may be skipped altogether in favor of a probiotic course of treatment. 

Probiotics of varying strains have been used for treating SIBO, but the more successful varieties I have found to be effective are:

  • Lactobacillus plantarum 299v which is in Metagenics Ultra Flora GI Regulate. The other ingredient is partially hydrolyzed Guar Gum (PHGG) - a water-soluble, prebiotic, FDA-approved dietary fiber.

Low Carbohydrate Diet

Following a low-carbohydrate diet helps reduce SIBO. (SIBO and migraines*). The main role of bacteria in the colon is to break down carbohydrates. If you lower your consumption of carbohydrates, you will give the bacteria less to feed on. 

“The list of food to avoid on the lactulose breath test kit basically includes everything bacteria enjoy: milk products, sugar, beans, legumes, soybeans, whole grains, corn, cornmeal, basmati and brown rice, pasta, dried fruit, nuts and seeds, and most vegetables. While avoiding all of these foods would be difficult, one would be well advised to avoid milk and sugar at the very least.” [3]

*A low carb diet can help reduce both SIBO and migraines, as carbohydrates are a well known migraine trigger. See point 6 below.

Enteric-coated Peppermint Oil

“Enteric-coated peppermint oil has been shown to be lethal to bacteria. In one case study, only ten days of treatment with enteric-coated peppermint oil resulted in not only a significant reduction in hydrogen production in the hydrogen breath test, but a reduction in bloating, pain, and belching. It is important to note that the peppermint oil must be enteric coated in order to avoid heartburn.” [3]

Increase Low Stomach Acid

Increasing your stomach acid could be vital. 

Luckily, increasing stomach acid is fairly easy. Supplementing with Betaine Hydrochloride (HCl) will increase stomach acid and aid the production of pancreatic enzymes. 

You can start with one tablet with a meal. If you get heartburn, stop and try again in a week or so. (Don't take the supplement before or after the meal, but during.) Stomach acid can also be aided by taking vitamin C with a meal, or by sipping a dilution of apple cider vinegar (ACV) in water (1 - 2 tablespoons ACV to 4 oz. or 120 mls of water). [3]

Pancreatic Enzymes

Pancreatic enzymes are important additions in SIBO treatments. “Enzymes are frequently under-utilized in people with SIBO, due to hypochlorhydria and bacterial deconjugation of bile. Supplementation with a broad-spectrum enzyme will aid the process of digestion and limit the substrate available to harmful bacteria. [3]

6 Natural Things That Help SIBO and Migraines

1. Remove food sensitivities and things that proliferate bacteria (this includes all fermented foods, even the ones you think are good for you). This will help reduce inflammation which effects migraine too.

2. Take HCL and enzymes so you can digest your food and avoid deficiency and low stomach acid.

3. Attend to your constipation. Keep that bacteria moving down and out. You can use: a salt flush or vitamin C flush, coffee enema; a salt flush followed by a coffee enema. [4]

My favorite product is Iberogast. It's a prokinetic. This is such a huge topic, I've written more here - Does Constipation Cause Migraine Headaches?

4. Close your ileocecal valve. "This is the 'border check' valve that keeps the microbial ecosystem of your colon separate from your small intestine. A lazy or flimsy valve is going to ensure the problem persists by letting bacteria up and into the small intestine where it doesn’t belong." [4]

The SIBO Doctor has a great video on Facebook that shows you exactly what to do... just wait for it to come into focus.

5. Finally a fun one... start doing some neuro-activation techniques like gargling, singing, and deep breathing that wake up the brain to help it remember it has role in intestinal motility. This should also help alleviate constipation. YAY! [4]

6. Limit carbohydrate consumption while you are ridding yourself of SIBO. Some carbohydrates can trigger a migraine attack too. Have you tested half a baked potato versus a whole one yet?

On that note, here's a great recipe... some help for dealing with SIBO and migraines.

SIBO Meal Plans From Rebecca CoomesMeal Plans for SIBO Eradication

SIBO Friendly Chicken Soup Recipe

A 2012 study in the American Journal of Therapeutics suggested that a compound called carnosine in chicken soup might be helpful during the early stages of viral illness. This recipe is a modified (SIBO-friendly) version of a traditional family recipe:

  • 2 large organic chicken breasts
  • 3 cups organic chicken stock or bone broth
  • 1 medium sized leek
  • 1 large carrot
  • 1 stalk of celery
  • 1 tsp-tbsp grated fresh ginger (depending on how much heat you like)
  • 1 tsp powdered ginger
  • 1 tbsp Garlic infused olive oil
  • 1 fresh of parsley (stems chopped finely to add into the stock and chop the leaves to add at the end of the cooking)
  • 1 lime (I'm allergic to lemon, so you can add either)
  • Sea salt and pepper to taste

Step 1

Thinly slice the chicken breasts while they are still frozen and set aside to thaw. This makes the chicken feel like noodles when you eat it and also creates a thicker soup. You can slice raw fresh chicken breasts if you have them or thaw the breasts first if you prefer.

Step 2

Chop the leek, carrot, celery and parsley stems. Heat a heavy pan and sauté the leek and fresh ginger until soft and aromatic, add the vegetables and sauté for 5 min.

Step 3

Add the chicken stock to the pot and bring it to a simmer. Add the sliced chicken and ½ of chopped parsley leaves and cook until the chicken is tender and white. It's best to check your biggest piece to see if it's cooked. Add salt and pepper to taste.

Serve sprinkled with fresh parsley and finely grated lime (or lemon) zest and wedges on the side. I like a little squeeze of lime juice in mine. I also sprinkle sesame seeds on top too.

If you are on Semi Restricted SIBO Diet you may add ¼ cup of cooked rice or quinoa to your bowl before ladling the hot soup over it.

SIBO and Migraines - 5 More Tips

If you suspect you might have SIBO, please see your doctor asap or seek a SIBO specialist.

  • Make notes on what symptoms you are having. Write them out manually in your migraine diary or use an app.
  • Be sure to note the frequency, intensity, and duration of the attacks, along with the other symptoms listed above that might indicate SIBO. 
  • List the medications and/or supplements you've been taking to help combat the additional symptoms of both SIBO and migraines. I.e. What you've been taking or doing to ease the constipation (fiber supplements, etc) diarrhea, or gas pain.

Here are 2 resources I use:

Until next time, be well and be pain free,


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How to be more migraine savvy right now...

SIBO and Migraines References:
1. DNM, Migraine Ireland (2019) Your Second Brain. Available [online] at:
2. Moore, C. (2014) Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome. Available [online] at:
3. Verrillo, Erica (2012-09-14). Chronic Fatigue Syndrome: A Treatment Guide, 2nd Edition (Kindle Locations 5954-5981). Erica Verrillo. Kindle Edition.
4. Orecchio, C. (2019) Is SIBO (Small Intestinal Bacterial Overgrowth) Causing Your Gut, Brain And Nervous System Issues? Available [online] at:
5. Cámara-Lemarroy, Carlos R et al. “Gastrointestinal disorders associated with migraine: A comprehensive review.” World journal of gastroenterology vol. 22,36 (2016): 8149-60. doi:10.3748/wjg.v22.i36.8149. Available [online] at:
SIBO and Migraines posted: Oct. 4, 2020. SIBO and Migraines Updated Sept. 18, 2021 | Feb. 13, 2024