Fibromyalgia, chronic pain and the role of the gut microbiome: new findings from 2025

12 Junho 2025

• Fibromyalgia
• Microbiome
• Chronic pain
• Clinical research

A study published in Neuron in 2025 and discussed on the TWIM (This Week in Microbiology) podcast on May 27th brought new evidence about the relationship between the gut microbiome and chronic pain in fibromyalgia. The work shows that changes in gut bacteria may not only be associated with, but also directly contribute to, pain and other symptoms of the disease.

Introduction: What is fibromyalgia and why does the microbiome matter?

Fibromyalgia is a common syndrome, marked by widespread pain, fatigue, sleep disturbances, and cognitive difficulties, mainly affecting women. It is estimated that fibromyalgia affects about 2% to 4% of the world population, being more prevalent in women between 30 and 60 years old. In Brazil, this represents millions of people living with chronic pain and a significant impact on quality of life, productivity, and healthcare costs. Fibromyalgia epidemiology: Fibromyalgia affects about 2% to 4% of the world population, being more common in women. In Brazil, millions of people are estimated to live with the syndrome, which is one of the main causes of chronic pain and disability. Despite its high prevalence, the causes of fibromyalgia are still poorly understood and available treatments are often unsatisfactory.

Why does the microbiome matter for health?

The gut microbiome is the set of trillions of microorganisms (mainly bacteria) that live in our digestive tract. It acts as a true “biochemical factory,” helping digest food, produce vitamins, regulate the immune system, and protect against infectious agents. In addition, the microbiome communicates with the brain through chemical substances and the enteric nervous system, influencing mood, metabolism, and even pain perception. Changes in the balance of these bacteria (dysbiosis) have been associated with several diseases, including metabolic, autoimmune, psychiatric disorders, and chronic pain conditions such as fibromyalgia. Gut microbiome: The gut microbiome is the set of trillions of microorganisms that inhabit the human gastrointestinal tract. The microbiome influences digestion, immunity, metabolism, and even the functioning of the nervous system.

Recent studies suggest that the gut microbiome can influence the functioning of the nervous and immune systems, even affecting pain perception.

Methods: How was the study conducted?

The researchers transplanted the microbiome (gut bacteria) from women with fibromyalgia into germ-free mice, comparing with transplants from healthy individuals. They also conducted a small open clinical study, in which women with fibromyalgia received microbiota transplants from healthy donors after antibiotic and bowel preparation.

Main results

In mice: Transplanting microbiota from fibromyalgia patients induced persistent pain, immune system changes, metabolic alterations, and reduced skin innervation—all phenomena similar to those observed in human patients. The mice showed increased sensitivity to mechanical, thermal (heat and cold), and spontaneous pain, without motor or cognitive changes. The study also showed that the patients’ microbiota led to changes in immune cells, activation of microglia in the spinal cord (cells involved in chronic pain), and changes in metabolites such as bile acids and neuroactive amino acids. Microglia: Microglia are cells of the central nervous system that act as “defenders” of the brain and spinal cord. When chronically activated, they can contribute to persistent pain and inflammation. When the mice later received microbiota from healthy people, the pain was reversed and part of the metabolic and immune changes returned to normal, suggesting a causal role of the microbiome in chronic pain in fibromyalgia.

Reversal: When the mice subsequently received healthy microbiota, the pain was relieved.

Figure 5 from the article: Graphs show that mice receiving microbiota from fibromyalgia patients had greater sensitivity to pain (mechanical, thermal, and spontaneous), and that subsequent transplantation of healthy microbiota reversed this, normalizing pain thresholds. Source: Cai W et al., Neuron, 2025.

In the clinical study: Women with severe, treatment-resistant fibromyalgia showed significant pain reduction and improved quality of life after receiving healthy microbiota transplants. The open clinical study involved 14 women, who received capsules of microbiota from healthy donors after bowel preparation. There was an average drop of 2 points on the pain scale (NRS), improvement in global disease impact (FIQ), reduction in anxiety and depression, better sleep, and improved physical quality of life. Sensory tests showed increased cold pain threshold and a trend toward improvement in heat pain. The metabolic profile and microbiome composition also changed, becoming more similar to the donors’. Adverse effects were mild and transient, mainly fatigue and mild gastrointestinal symptoms. Fecal Microbiota Transplantation (FMT): A procedure in which gut bacteria from a healthy donor are transferred to the intestine of a patient, aiming to restore the balance of the microbiome. It is already used to treat Clostridioides difficile infections and is under study for other conditions.

Figure 6 from the article: Graphs show that after healthy microbiota transplantation, women with fibromyalgia had significant reduction in pain intensity, improvement in global disease impact, anxiety, depression, sleep quality, and physical quality of life. The graphs also show changes in cold and heat pain thresholds. Source: Cai W et al., Neuron, 2025.

Significance for the field and for patients

The study provides evidence that the gut microbiome is not just a “bystander” in fibromyalgia, but may be one of the factors causing or perpetuating chronic pain. This opens the way for new therapeutic approaches, such as microbiota transplantation or the use of specific probiotics, and reinforces the importance of research on the relationship between the gut, immune system, and brain. Probiotics: These are live microorganisms that, when administered in adequate amounts, confer health benefits. They can modulate the gut microbiome and are being studied as a complementary therapy in chronic diseases.

Despite the promising results, it is important to remember that the clinical study was small and open-label (without a control group), and more research is needed before microbiota transplantation can be routinely recommended. Still, the work represents an important advance in understanding fibromyalgia and may inspire new strategies to treat chronic pain.

What is TWiM?

TWiM (This Week in Microbiology) is a podcast created by virologist Vincent Racaniello, from Columbia University (USA), in 2010. The program discusses weekly advances and curiosities in microbiology, focusing on recent scientific articles and topics relevant to health and science. The regular members include:

• Vincent Racaniello (Columbia University, USA)
• Petra Levin (Washington University in St. Louis, USA)
• Michele Swanson (University of Michigan, USA)
• Michael Schmidt (Medical University of South Carolina, USA)

All are recognized scientists in their fields. TWiM is part of the MicrobeTV network and is available for free at microbe.tv/twim.

References:

• Original article in Neuron
• TWIM 332: Fibromyalgia pain and the gut microbiome