Summary: A Montreal research team used clinical methods and deep learning to identify consistent changes in the gut microbiome of people with fibromyalgia. These alterations were independent of diet, medication, or age, and the degree of symptom severity correlated with the presence or absence of specific bacterial species.
Source: McGill University
Altered gut bacteria linked to fibromyalgia
Researchers have reported a clear association between fibromyalgia—a chronic pain disorder affecting an estimated 2–4% of the population—and measurable changes in the gastrointestinal microbiome. In a study published in the journal Pain, the Montreal-based team found approximately 19–20 bacterial species that differed consistently between people with fibromyalgia and matched healthy controls. Some species were present at higher levels, while others were reduced or absent in patients.
Distinct microbial patterns not explained by lifestyle or medications
Using a combination of genomic analysis and machine learning, the investigators controlled for common factors known to shape the microbiome, including diet, medication use, physical activity and age. “The microbiome differences we observed could not be explained by these other variables,” says Dr. Amir Minerbi of the Alan Edwards Pain Management Unit at the McGill University Health Centre, first author of the paper. The study team included clinicians and geneticists from McGill University, Université de Montréal and the Research Institute of the MUHC.
Importantly, variation in the microbiome was more strongly associated with fibromyalgia and its hallmark symptoms—pain, fatigue and cognitive difficulties—than with any other measured factor. The researchers also discovered that greater symptom severity corresponded to a larger abundance change (either an increase or a pronounced decrease) in certain bacterial species, a correlation not previously reported.
Marker or mechanism: open questions
At present, it remains uncertain whether the microbiome changes are markers that reflect the disease state or whether they play a causal role in the development or perpetuation of fibromyalgia. Because fibromyalgia presents as a syndrome with multiple systemic symptoms rather than a single localized disorder, the team plans to compare these findings with microbiome profiles from other chronic pain conditions—such as chronic low back pain, migraine and neuropathic pain—to determine whether similar microbial signatures are present.
Future work will also investigate whether manipulating specific bacteria can influence pain pathways or symptom progression, and whether bacterial signatures might be used to guide new treatments or prevention strategies.
Potential for improved diagnosis
Fibromyalgia is notoriously difficult to diagnose; many patients wait several years to receive a definitive diagnosis. In this study, Emmanuel Gonzalez from the Canadian Center for Computational Genomics and McGill’s Department of Human Genetics reports that machine learning models trained on microbiome composition alone could distinguish fibromyalgia patients from controls with about 87% accuracy. While preliminary, this result suggests microbiome-based biomarkers could eventually help clinicians make faster, more objective diagnoses when combined with clinical assessment.
Study design and next steps
The study analyzed samples from 156 Montreal-area participants, including 77 individuals diagnosed with fibromyalgia and 79 controls. Participants provided stool, blood, saliva and urine samples and completed clinical interviews. Some controls were household members or relatives of patients to reduce environmental and familial confounders. Microbiome profiling used 16S rRNA gene sequencing and whole genome sequencing, complemented by targeted serum metabolite analysis that showed differences in compounds related to butyrate and propionate metabolism—metabolic pathways linked to certain altered bacterial groups.
The authors plan to replicate these findings in independent cohorts from other geographic regions and to pursue animal studies that can test whether changing microbiome composition alters pain outcomes. Such experiments are needed to move beyond correlation and toward understanding potential mechanisms.
Funding and publication details
This research was funded by the Louise and Alan Edwards Foundation and the Israeli Society for Musculoskeletal Medicine. The study, titled “Altered microbiome composition in individuals with fibromyalgia,” appears in the journal Pain (doi: 10.1097/j.pain.0000000000001640). Lead authors include Amir Minerbi, Emmanuel Gonzalez and Yoram Shir, among others.
Clinical implications
These findings add to a growing body of evidence linking the gut microbiome with central nervous system processes and chronic pain. While clinical applications are not immediate, the ability to identify a reproducible microbial signature associated with fibromyalgia opens new avenues for diagnostic development and for research into microbiome-targeted interventions that could complement existing symptom management strategies.