The Gut-Pain Connection – alive magazine

Chronic pain affects millions of Canadians, yet it’s largely treated as a problem of muscles, joints, or nerves—leaving the gut out of the conversation. Emerging research, however, shows that the gut microbiome plays a powerful role not just in inflammation, but also in how pain is perceived and processed.

Gut-brain-pain axis

“The gut and brain are in constant two-way communication through what’s known as the gut-brain axis,” says Dominique Vanier, ND. “This communication occurs through multiple pathways, including the nervous system, particularly the vagus nerve; immune signalling; hormones; and metabolites produced by the gut microbiota.

“The gut microbiome plays an important role in this communication,” says Vanier. “Certain bacteria can produce or influence neurotransmitters such as serotonin, dopamine, and GABA, which affect mood, stress responses, and how the brain processes pain.”

Vanier, who practises in Ontario’s Oakville-Burlington region, has educated more than 700 clinicians across Canada on digestive health, covering topics such as disorders of gut-brain interaction, including irritable bowel syndrome (IBS).

Beyond influencing neurotransmitters, the compounds produced by gut bacteria—such as metabolites, neuromodulators, and neuropeptides—can interact with the body’s pain receptors, shaping how chronic pain develops and persists.

“Gut microbes also interact with the immune system and influence inflammatory signalling throughout the body,” says Vanier.

When the gut is out of balance

The gut-brain axis doesn’t work in our favour if we’re dealing with gut dysbiosis. This refers to a decrease in the diversity of microbiota, a loss of beneficial microbiota, or an overgrowth of harmful microbiota.

Gut dysbiosis is associated with various chronic pain disorders, such as visceral pain, neuropathic pain, migraine, fibromyalgia, and inflammatory pain.

Migraine

Evidence suggests that the gut-brain axis influences migraine through inflammatory mediators, stress hormones, serotonin, neuropeptides, and the gut microbiota and its metabolites.

While research has established that gut dysbiosis influences migraine, a 2025 study suggests that oral dysbiosis may be even more pronounced than gut dysbiosis among migraine sufferers. Although the mouth and the intestines are physiologically distinct, they are directly connected. Microorganisms in the mouth can colonize the digestive tract and contribute to gut dysbiosis.

Fibromyalgia

Fibromyalgia is characterized by widespread, chronic pain and affects millions of people worldwide.

A 2026 systematic review reported an imbalance in gut microbiota among fibromyalgia patients and a significant difference in microbial diversity and gut permeability (leaky gut) compared to healthy controls.

Gut dysbiosis and gut permeability are associated with emotional, cognitive, and somatic symptoms of psychological distress in fibromyalgia patients.

Inflammatory joint pain

While we used to think that osteoarthritis (OA) arose only from injury or aging, recent research into the pathogenesis of OA reveals that gut dysbiosis, chronic low-grade inflammation, and alterations in central pain-processing centres are also contributing factors.

Alterations in intestinal bacteria have been found in those with rheumatoid arthritis (RA), suggesting that the gut microbiota play a role in the immune dysfunction that’s characteristic of the disease. Microbial infection is considered a crucial inducer of RA.

Contributors to gut dysbiosis

“Dysbiosis rarely has a single cause,” says Vanier. “It can develop due to a combination of microbiome disruption, immune changes, altered gut-brain signalling, and genetic makeup.”

An individual’s health status (including infections and inflammation); lifestyle factors, such as diet (high-sugar, low-fibre); hygiene; and xenobiotic exposure (food additives, nonsteroidal anti-inflammatory drugs, opioids, and antibiotics) may all contribute to dysbiosis. Even a single course of antibiotics can alter the microbiome for up to eight years.

“Because the gut and brain communicate so closely, stress can also reshape the microbiome and amplify digestive symptoms,” says Vanier. “People with a history of adverse childhood experiences are at an increased risk of developing a disorder of gut-brain interaction.”

How food shapes pain signalling

Inflammatory pain arises due to an increased sensitivity of perception to harmful stimuli. Using food to shape pain signalling depends primarily on eating to reduce inflammation.

Eating ultraprocessed foods, characterized by a high content of synthetic additives and emulsifiers, and low fibre intake are associated with decreased microbial diversity and an increase in pro-inflammatory microorganisms.

This microbial makeup contributes to persistent inflammation, which is associated with chronic disorders including IBS, type 2 diabetes, metabolic syndrome, and colorectal cancer.

“Dietary patterns that support gut health and reduce systemic inflammation tend to include a wide variety of plant foods; both soluble and insoluble fibre; and minimal ultraprocessed foods, which helps maintain a resilient and diverse microbiome,” says Vanier.

The Mediterranean diet, which emphasizes plant foods and healthy fats, is associated with a reduction in systemic inflammation.

Soluble fibres (found in avocados, oats, black beans, and flaxseeds) are metabolized by gut bacteria to produce short-chain fatty acids (SCFAs). SCFAs maintain intestinal-barrier integrity and regulate inflammation.

Research into the relationship between chronic pain and micronutrient deficiencies suggests that B vitamins (found in meat, fish, legumes, eggs, and leafy greens) play a role in maintaining the health of the nervous system and pain-signalling pathways.

Ensuring proper hydration is also key for chronic pain management, as dehydration increases sensitivity to pain.

This article was originally published in the July 2026 issue of alive magazine.