Gut bacteria and migraine

September 18, 2023

Most people have heard about the gut-brain connection. Research published in The Journal of Headache and Pain examined this connection in relation to migraine headaches. The researchers looked at whether the collection of microorganisms living in our guts (called the gut microbiome) could be linked to the development of migraine headaches and its different types – migraine with and without aura.

To do this, the scientists used information from a big genetic study that looked at the genes related to the gut microbiome. They also used data from studies that explored the genetics of migraine headaches. They employed sophisticated methods to analyze this data, and they also checked for other factors that could affect the results.

In the analysis, they found that certain types of bacteria in the gut were connected to migraine headaches, including ones with and without aura. They also found that some specific types of bacteria were more likely to be associated with certain types of migraines. Even after doing some statistical adjustments, these connections still held up.

So, this study suggests that the mix of bacteria in our guts might actually influence whether we get migraines and what kind they are. It shows that there might be a link between our gut and our brain when it comes to migraines.

They found that while some bacteria seemed to contribute to migraines, one type appeared to be protective. This protective effect was linked to the Bifidobacterium family. You can find Bifidobacterium in many probiotics, including a well-known brand called Align. Additionally, various fermented foods like milk kefir, sourdough bread, sauerkraut, kimchi, and other fermented vegetables contain Bifidobacterium.

However, it’s important to note that this research doesn’t mean other types of bacteria aren’t helpful too. A healthy human gut microbiome consists of many different types of bacteria. When there is an imbalance of these healthy bacteria, it can lead to various health problems, not just migraines. This imbalance can come in many different forms and may require different probiotics to correct it. That is why I recommend that patients try different types of probiotics for a few months at a time. Besides Bifidobacteria, some patients respond well to Saccharomyces, Lactobacillus, or other types, or even a combination of several.

Written by
Alexander Mauskop, MD
Continue reading
May 21, 2026
Research
Your Brain Has Many Pathways, And TMS Can Now Use Them
A groundbreaking University of Iowa study shows that personalized fMRI-guided TMS can now reach and modulate the deep hippocampus — the brain’s command center for memory, emotion, and migraine — without surgery or heavy medications. By mapping each patient’s unique neural pathways, TMS delivers precise stimulation to surface “control points” that influence deep brain structures. Generic approaches barely work, but individualized targeting produces clear, measurable changes. At our headache clinic, we combine TMS and fMRI to offer this advanced, personalized treatment for migraines, depression, PTSD, anxiety, and more.
Read article
May 10, 2026
Research
Elismetrep: A Promising New Experimental Migraine Treatment
Elismetrep is a promising experimental migraine medication that targets the TRPM8 pathway rather than serotonin or CGRP. Early clinical trials suggest it may offer a new option for patients who do not respond well to current treatments.
Read article
May 6, 2026
Alternative Therapies
New Research on Brain Excitability and TMS Treatment for Migraine
New research shows how the brain dynamically regulates excitability in real time—and why this matters for transcranial magnetic stimulation (TMS) as a treatment for migraine.
Read article
Insights from Dr. Alexander Mauskop on headaches and migraines
Subscribe to the Blog.
Subscribe
Subscribe