The Gut-Brain Connection: What It Means for Migraine

Most people think migraine is just a strong headache. We, in the Migraine Buddy community, know that it’s a neurological condition. But here’s something that often comes as a surprise: your digestive system might be part of what’s happening. Researchers have spent the last decade piecing together a picture of just how much the gut and brain are in conversation with each other, and what that means for people who live with migraine.

If you’ve ever noticed that an attack tends to follow a rough night of eating, or that nausea is as much a part of your attacks as the headache itself, you’ve already felt this connection. Science is now beginning to explain why.

The Gut and Brain Share a Private Line

The gut and the brain are in constant, two-way communication through what researchers call the gut-brain axis. This is not a metaphor. It is a real biological network made up of neural pathways, hormonal signals, and immune messengers that shuttle information back and forth between your digestive tract and your central nervous system [1].

The main highway in this system is the vagus nerve, a long nerve that runs from the brainstem all the way down into the abdomen and relays signals in both directions. Research has shown that when certain types of bacteria are removed from the gut, it actually changes the expression of receptors in the brain. It is a striking demonstration of just how dependent these two organs are on each other [2].

The gut is also home to roughly 100 trillion microorganisms (bacteria, fungi, and other microbes) that together make up your gut microbiome [3]. These microbes are not passive passengers. They produce neurotransmitters including serotonin and dopamine, which influence mood and pain perception [4]. Notably, about 90% of the body’s total serotonin is produced in the gut, not the brain.

Beyond neurotransmitters, the microbiome produces molecules called short-chain fatty acids (SCFAs). Think of them as tiny chemical signals: they travel through the bloodstream, cross into the brain, and influence how it functions [5]. A healthy, diverse microbiome keeps this signalling stable. When the balance of gut bacteria is disrupted (a state researchers call dysbiosis) that stability breaks down, and the effects don’t stay in the stomach.

What a Disrupted Gut Can Do to Migraine

People who live with migraine are significantly more likely than the general population to also have gastrointestinal conditions. A 2023 meta-analysis found that people with irritable bowel syndrome (IBS) are more than twice as likely to experience migraine, and people with migraine are about 2.5 times more likely to have IBS [6]. This is not a coincidence. Both conditions appear to involve the same underlying mechanisms, including central sensitisation and gut-brain axis dysfunction.

When the gut microbiome is out of balance, several things happen that can directly affect migraine.

• First, a disrupted gut lining can become more permeable (sometimes called a “leaky gut“), allowing bacterial fragments and undigested proteins to enter the bloodstream [7].

The immune system reads these particles as foreign invaders and mounts a response, creating inflammation throughout the body. That inflammation reaches the trigeminal nerve system and triggers the release of CGRP — the protein so central to migraine pain that several modern medications work specifically by blocking it [1].

• Second, gut dysbiosis disrupts how the body regulates serotonin.

Remember that 90% of the body’s serotonin is made in the gut. When the gut barrier is compromised, serotonin release becomes erratic. That abnormal release travels up the vagus nerve and disturbs the same nerve system involved in migraine pain [5].

• Third, stress, a well-known migraine trigger, directly affects the microbiome.

When you’re stressed, your body releases cortisol, which directly affects the gut: it makes the gut lining more permeable and shifts the balance of bacteria [8]. This creates a loop: stress disrupts the gut, the gut drives inflammation, and inflammation makes a migraine attack more likely.

What We Know About Treating the Gut to Help Migraine

There is no cure for migraine, and treating the gut alone is not going to replace the care of a neurologist. What is growing, however, is solid evidence that gut-targeted approaches can reduce attack frequency and severity.

Probiotics

The most studied option. A 10-week randomised double-blind controlled trial using a 14-strain probiotic found reduced attack frequency and severity in both episodic and chronic migraine, with stronger results in chronic migraine [9]. Two 2024 trials (one in children, one in adults) found similar benefits, particularly when probiotics were combined with standard treatment or vitamin D [10, 11].

However, not all studies agree. A 2020 meta-analysis found no statistically significant effect overall [12]. The strain, duration, and your migraine type all seem to influence whether it works.

Diet

A 2025 study of over 7,600 people with migraine and digestive issues found that a low-FODMAP, low-starch, low-sucrose diet led to meaningful migraine improvement in 60% of participants after just two weeks, with pain intensity dropping from 6.1 to 3.8 on average [13].

Omega-3 fatty acids also have solid backing. A 2024 randomised trial found that higher omega-3 intake from food (not supplements) correlated with less migraine pain, likely by reducing neuroinflammation [14]. The Mediterranean and ketogenic diets have both shown early promise for similar reasons [15].

Fecal microbiota transplantation (FMT)

Still experimental. FMT involves transferring gut bacteria from a healthy donor, and preliminary evidence suggests it could help restore the serotonin and inflammatory pathways disrupted in migraine [3]. It is not a standard treatment option yet.

6 Things You Can Start Doing Now

None of these replace medical treatment, but all of them are supported by evidence and are worth discussing with your doctor.

1. Track your gut alongside your head

If you use Migraine Buddy to log your attacks, start adding notes about your digestion in the days before an attack. Constipation, bloating, or diarrhoea often appear in the prodrome (the hours or days before pain begins), and spotting this pattern can help you and your doctor understand your triggers more clearly.

2. Add fermented foods to your regular diet

Yoghurt, kefir, sauerkraut, miso, and kimchi introduce beneficial bacteria into the gut naturally. A 2021 randomised trial published in Cell found that a high-fermented-food diet increased microbial diversity and reduced inflammatory markers after just 10 weeks [16]. More diversity in your microbiome is consistently associated with lower rates of migraine.

One thing to keep in mind: fermented foods are high in histamine, which is a known trigger for some people. If you suspect histamine sensitivity, start small and see how your body responds.

3. Feed the good bacteria with fibre

Dietary fibre from vegetables, legumes, and whole grains is what gut bacteria eat to protect both the gut lining and brain function. If your diet is currently low in fibre, increase it gradually to avoid any digestive discomfort while your microbiome adjusts.

4. Consider whether a low-FODMAP approach is worth exploring

FODMAPs are fermentable carbohydrates found in foods like onions, garlic, wheat, and certain fruits. For people who have both migraine and IBS or bloating, reducing FODMAP intake may reduce gut-driven inflammatory signals. The evidence for this specifically in migraine is growing [13].

Note: this is worth doing with a dietitian rather than alone, especially if you’re also experimenting with fermented foods, since many of them are high in FODMAPs and the two approaches don’t always combine easily.

5. Protect your microbiome from unnecessary disruption

Antibiotics, chronic stress, poor sleep, and a high-processed-food diet all reduce microbial diversity. You may not be able to control all of these, but being aware of how they affect your gut and your migraine is a practical starting point. Sleep and stress management in particular are already known to affect attack frequency, and gut health gives you another reason to take them seriously.

6. Talk to your doctor before starting probiotics

Probiotics are generally safe but the research is specific enough that strain selection matters. Telling your neurologist or GP that you are interested in gut-targeted approaches opens a conversation about whether a specific supplement or dietary change makes sense for your individual pattern of attacks.

Please remember that this article is for educational purposes and is not medical advice. Always consult with your healthcare provider before making significant changes to your diet or starting new supplements.

References

[1] Arzani M, et al. “Gut-brain axis and migraine headache: a comprehensive review.” Journal of Headache and Pain, 2020. https://doi.org/10.1186/s10194-020-1078-9

[2] Crawford J, Liu S, Tao F. “Gut microbiota and migraine.” Neurobiology of Pain, 2022. https://doi.org/10.1016/j.ynpai.2022.100090

[3] Kappéter Á, et al. “Migraine as a Disease Associated with Dysbiosis and Possible Therapy with Fecal Microbiota Transplantation.” Microorganisms, 2023. https://doi.org/10.3390/microorganisms11082083

[4] Mugo CW, et al. “Unravelling the gut-brain connection: a systematic review of migraine and the gut microbiome.” Journal of Headache and Pain, 2025. https://doi.org/10.1186/s10194-025-02039-7

[5] Stilling RM, et al. “Short chain fatty acids: Microbial metabolites for gut-brain axis signalling.” Molecular and Cellular Neuroscience, 2022. https://doi.org/10.1016/j.mcn.2022.103764

[6] Tan YM, et al. “Systematic review and meta-analysis of calculating degree of comorbidity of irritable bowel syndrome with migraine.” BioPsychoSocial Medicine, 2023. https://doi.org/10.1186/s13030-023-00275-4

[7] Nguyen L, et al. “The gut-brain connection and episodic migraine: an update.” Current Pain and Headache Reports, 2023. https://doi.org/10.1007/s11916-023-01175-6

[8] Riehl L, et al. “The importance of the gut microbiome and its signals for a healthy nervous system.” Frontiers in Neuroscience, 2024. https://doi.org/10.3389/fnins.2023.1302957

[9] Martami F, 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. https://doi.org/10.1177/0333102418820102

[10] Bazmamoum H, et al. “Efficacy of Probiotics in Prevention of Migraine Attacks in Children: A Randomized Clinical Trial Study.” Iranian Journal of Child Neurology, 2024. https://doi.org/10.22037/ijcn.v17i4.39598

[11] Tirani SA, et al. “Effects of probiotic and vitamin D co-supplementation on clinical symptoms, mental health, and inflammation in adult patients with migraine headache: a randomized, triple-blinded, placebo-controlled trial.” BMC Medicine, 2024. https://doi.org/10.1186/s12916-024-03684-6

[12] Parohan M, et al. “Effect of probiotic supplementation on migraine prophylaxis: a systematic review and meta-analysis of randomized controlled trials.” Nutritional Neuroscience, 2020. https://doi.org/10.1080/1028415X.2020.1764292

[13] Pereyra F, et al. “Gut-brain axis and migraine: rates of improvement and predictors of response after a low-FODMAP, low-starch and low-sucrose dietary intervention.” Journal of Human Nutrition and Dietetics, 2025. https://doi.org/10.1111/jhn.70104

[14] Wang HF, et al. “Associations Between Dietary Intakes of Omega-3 Fatty Acids, Blood Levels, and Pain Interference in People with Migraine.” Nutrients, 2025. https://doi.org/10.3390/nu18010003

[15] Olivito I, et al. “Mediterranean ketogenic diet accounts for reduced pain frequency and intensity in patients with chronic migraine: a pilot study.” Clinical Nutrition, 2024. https://doi.org/10.1016/j.clnu.2024.06.015

[16] Wastyk HC, et al. “Gut-microbiota-targeted diets modulate human immune status.” Cell, 2021. https://doi.org/10.1016/j.cell.2021.06.019