Bad Gut Bacteria Causes Headaches And Migraines

mbg senior sustainability Editor

By Dr.lauryn

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Headaches and migraines got you down? The answer to curing them may be in your gut…not your head.

Headaches And Migraines 101 

Headaches and migraines are among the most common neurological disorders worldwide, affecting approximately 50% of all adults every month, with prevalence among women more than twice as high as among men.

A headache is a “pain felt in the head, characterized by common characteristics including: throbbing, squeezing, constant, unrelenting, or intermittent. Headaches are an inflammatory response in the body, most headaches happen in the nerves, blood vessels, and muscles that cover a person’s head and neck.

woman sitting on the floor suffering from headaches and migraines

Although it may seem like it, a headache is not actually a pain in your brain. Instead, the brain tells you when other parts of your body hurt or are inflamed; your brain doesn’t necessarily physically experience the pain itself (it just feels like).

Why are some people more susceptible to experiencing inflammation in the form of headaches and migraines more than others? The answer may lie in what scientists call the “gut brain axis.”

The Gut-Brain Connection

The brain and gut are connected through a variety of pathways, including the enteric nervous system (ENS), vagus nerve, the immune system, or the metabolic processes of gut microorganisms. The pain you feel during a headache comes from a mix of signals between all of these parts: your brain, blood vessels, nearby nerves, and believe it or not, your gut.

Gut as the second brain.

The gut is often referred to as the “second brain” in the scientific literature:

  • You have more than 100 million neurons in your gut—cells and signals that talk directly to the brain. 
  • More than 90% of your serotonin (your “feel good” brain chemicals) that calms inflammation in the body is produced in your gut.
  • Your vagus nerve, the nerve that governs your digestive process and your brain frontal lobe (“clear thinking”) function is directly connected from the top of your stomach to the top of your brain.
  • Your liver (your body’s #1 anti-inflammatory and cleansing organ) detoxifies unwanted toxins out of your body. It also metabolizes hormones (like cortisol, your stress hormones) and manufactures most of your neurotransmitters (including serotonin, your “feel good: brain chemical). However if your liver is sluggish, congested or overworked (from too many toxins, pesticides, non-organic foods, artificial sweeteners, longterm medication use, environmental stressors, etc.), then your brain (and headaches) suffer. Your hormone balance (cortisol levels) and neurotransmitters (brain chemicals) are unable to function properly.

In short:

Specific nerves of the blood vessels and head muscles switch on and send pain signals to your brain.  Although there are tons of different triggers to headaches and the “mixed signals” in the brain, blood vessels, nerves and gut, all headaches share one root cause: Inflammation, or stress, inside your body. 

The Result:

  • Your neurons are unable to fire properly.
  • Your cortisol (inflammation fighting hormone) is in “stressed out mode.”
  • Also, your “feel good” anti-inflammatory brain chemicals are suppressed.
  • You get headaches.

The Gut-Headache Connection Facts

Check out some of these interesting clinical and observational findings:

Migraine sufferers have different bacteria from those without migraines.

One study (1) showed that migraine sufferers had higher levels of bacteria that are known to be involved in processing nitrates, which are typically found in processed meats, leafy vegetables and some wines, raising the possibility that migraines could be triggered when nitrates in food are broken down more efficiently, provoking vessels in the brain and scalp to dilate.

When nitrates in food are broken down by bacteria in the mouth and gut they are eventually converted into nitric oxide in the blood stream, a chemical that dilates blood vessels and can aid cardiovascular health by boosting circulation. 

Migraines are not “just genetic.”

In only 20% of identical twins do migraines show up in both or neither twins (2).

This suggests that genetics are only part of the picture. The rest of the picture is made up of environmental factors, including gut bacteria.

Different types of headaches are connected to different digestive organs.

Traditional Chinese Medicine relates different types of headaches to inflammation experienced in different organs—particularly digestive organs. For instance, headaches that occur as part of PMS are also related to Liver function, which is responsible for flow—both of blood and emotions.

Early research supports that estrogen production (or lack thereof), which primarily occurs in the liver, may affect the onset of headaches in approximately 60% of women around menstruation (3). Researchers looked at urine samples of 114 women with migraines and 223 women without migraines, average age 47. Estrogen levels among those with migraines dropped 40 percent in the days just before menstruation, compared to 30 percent for those without migraines, the study found (4).

Another example is headaches that strike after eating, particularly in the front of the forehead; According to Chinese Medicine, this generally indicates you are suffering from a Stomach Qi deficiency, like low stomach acid. Your Stomach is lacking the Qi or energy to digest food properly.

Research on patients with GERD, reflux or heartburn (conditions all linked to low stomach acid) have found that more than 50% of these patients experience headaches when symptoms strike (5, 6). 

The Gut-Brain Connection Roles

The “gut-brain” connection plays a big role in how your body experiences stress and inflammatory process experienced in your brain and body when headaches strike. You will have high chances of  having headaches and migraines. If your gut health is “out of whack” and you have lots of inflammation in your gut, guess where you may experience that inflammation? Your brain.


  1. Correction for Gonzalez et al. (2017). “Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort”. mSystems, 2(2), e00023-17. doi:10.1128/mSystems.00023-17
  2. van Hemert, S., Breedveld, A. C., Rovers, J. M., Vermeiden, J. P., Witteman, B. J., Smits, M. G., & de Roos, N. M. (2014). Migraine associated with gastrointestinal disorders: review of the literature and clinical implications. Frontiers in neurology, 5, 241. doi:10.3389/fneur.2014.00241
  3. National Headache Foundation. 2018. Menstrual Migraine. 
  4. Katić, B. J., Golden, W., Cady, R. K., & Hu, X. H. (2008). GERD prevalence in migraine patients and the implication for acute migraine treatment. The journal of headache and pain, 10(1), 35-43.
  5. Pavlović, J. M., Allshouse, A. A., Santoro, N. F., Crawford, S. L., Thurston, R. C., Neal-Perry, G. S., Lipton, R. B., … Derby, C. A. (2016). Sex hormones in women with and without migraine: Evidence of migraine-specific hormone profiles. Neurology, 87(1), 49-56.
  6. T Noghani, M., Rezaeizadeh, H., Fazljoo, S. M., & Keshavarz, M. (2016). Gastrointestinal Headache; a Narrative Review. Emergency (Tehran, Iran), 4(4), 171-183.

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