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Can Gut Health Affect Headaches?

The gut-brain axis is bi-directional and the health of the gut is thought to affect headaches and migraines.

The gut-brain axis is bi-directional and is thought to play a role in the causation of migraines and headache.1 However, the mechanisms explaining how the gut and the brain may interact in patients with migraines and headaches are not entirely clear. Studies suggest that this interaction is influenced by multiple factors such as inflammatory mediators (IL-1β, IL-6, IL-8, and TNF-α), gut microbiota profile, neuropeptides and the serotonin pathway, stress hormones and nutrients. Based upon animal research, it is suspected that increased inflammation resulting from dysbiosis, might worsen migraine pain.2

Inflammation resulting from dysbiosis, might worsen migraine pain

Alpha diversity is decreased in people suffering from migraine, along with higher levels of Firmicutes, especially pathogenic Clostridia species, while healthy controls have more ‘beneficial’ bacteria; Faecalibacterium prausnitzii, Bifidobacterium adolescentis, and Methanobrevibacter smithii.3 People with a history of headache and migraine also have higher rates of irritable bowel syndrome, and migraines are also associated with inflammatory bowel disease.4

Additionally, in an older trial, children with migraine had significantly greater intestinal permeability than those without.5

Are probiotics beneficial for migraines?

While several randomised trail have shown reduced frequency and severity of migraine attacks with probiotic supplement use6, 7 (notably without changes in inflammation or intestinal permeability), a systematic review of the available trials published in 2020 found no significant effect of probiotic supplementation on migraines.8

How can people with migraine support the microbiome?

The following tactics have been suggested for microbiome support impacting migraine headaches4:

  • Experiment with a gluten-free diet
  • Increase fibre and resistant starch intake
  • Reduce the glycaemic (sugar/carb) load of the diet
  • Supplement with vitamin D, omega-3 (fish oil) and probiotics
  • Support healthy weight-loss and weight management if overweight or obese (holding body fat levels likely to increase adipokine-driven inflammation)


1.         Hindiyeh N, Aurora SK. What the Gut Can Teach Us About Migraine. Current Pain and Headache Reports. 2015;19(7):33.

2.         Tang Y, Liu S, Shu H, Yanagisawa L, Tao F. Gut Microbiota Dysbiosis Enhances Migraine-Like Pain Via TNFα Upregulation. Molecular Neurobiology. 2020;57(1):461-8.

3.         Chen J, Wang Q, Wang A, Lin Z. Structural and Functional Characterization of the Gut Microbiota in Elderly Women With Migraine. Frontiers in Cellular and Infection Microbiology. 2020;9(470).

4.         Arzani M, Jahromi SR, Ghorbani Z, Vahabizad F, Martelletti P, Ghaemi A, et al. Gut-brain Axis and migraine headache: a comprehensive review. The Journal of Headache and Pain. 2020;21(1):1-12.

5.         Amery W, Forget P. The Role of the Gut in Migraine: The Oral 51–Cr EDTA Test in Recurrent Abdominal Pain. Cephalalgia. 1989;9(3):227-9.

6.         Martami F, Togha M, Seifishahpar M, Ghorbani Z, Ansari H, Karimi T, et al. The effects of a multispecies probiotic supplement on inflammatory markers and episodic and chronic migraine characteristics: A randomized double-blind controlled trial. Cephalalgia. 2019;39(7):841-53.

7.         De Roos N, Van Hemert S, Rovers J, Smits M, Witteman B. The effects of a multispecies probiotic on migraine and markers of intestinal permeability–results of a randomized placebo-controlled study. European journal of clinical nutrition. 2017;71(12):1455-62.

8.         Parohan M, Djalali M, Sarraf P, Yaghoubi S, Seraj A, Foroushani AR, et al. Effect of probiotic supplementation on migraine prophylaxis: a systematic review and meta-analysis of randomized controlled trials. Nutritional neuroscience. 2020:1-8.

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