Myalgic encephalomyelitis (ME), also known as chronic fatigue syndrome (CFS), or ME/CFS, is a debilitating illness of unknown etiology with no widely accepted therapy. Primary symptoms reported by patients are fatigue, muscle and/or joint paint, sore throat, headaches, unrefreshing sleep, and post-exertional malaise and have been the basis of the widely used Fukuda diagnostic criteria. Many ME/CFS patients also report gastrointestinal (GI) symptoms, including but not limited to irritable bowel syndrome (IBS).1

Intestinal discomfort is also indicated in a survey of drug use by individuals with CFS compared to controls, which found significantly more use of antacids, H2 blockers, and proton pump inhibitors in the ME/CFS cohort.2

New research posted in the Open Access Microbiome journal suggests that there is a correlation of these symptoms to the state of the intestinal flora. It has been difficult to pinpoint exactly which species are responsible but there are some trends:

Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome1

Taken together, our results suggest an ongoing damage to the gut mucosa, leading to increased microbial translocation in ME/CFS, which in turn could alter antimicrobial regulators and disregulate the innate immune system.

Differences between the gut microbiomes of healthy individuals and patients with ME/CFS were identified in terms of relative abundance of specific genera. There is no single precise alteration of the gut microbiota in all ME/CFS patients we examined, but our data converges to support the concept of a less diverse and unstable community of bacteria in the disorder. It highlights the association of specific bacterial taxa with E/CFS, and the identification of the underlying role of this altered commensal gut microbiota could lead to novel diagnostic and therapeutic strategies that would improve clinical outcome. Future studies may also reveal additional molecular markers that could be combined with gut microbiome information to enhance the sensitivity and specificity of ME/CFS diagnostic assays.

The cause of ME/CFS is unknown, but gut dysbiosis could be contributing to some of the symptoms and their severity. Developing therapeutic interventions aimed at reducing local inflammation, restoring gastrointestinal tract immunity and integrity and modifying the intestinal microbiome may ameliorate ME/CFS symptoms in a number of affected patients.

Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome2

Our results confirm and extend previous work indicating intestinal dysbiosis in ME/CFS. We further demonstrate that patterns of dysbiosis vary with IBS co-morbidity. Future prospective studies should consider more detailed exploration of IBS subtypes, associated GI symptoms, and their relationship to ME/CFS dysbiosis. The identification of ME/CFS networks characterized by specific profiles that integrate microbiota, metabolic pathways, and plasma immune molecules may enable more accurate diagnosis and lead to insights that inform the development of specific therapeutic strategies.

Our Opinion

Sometimes patients who believe they have chronic fatigue syndrome are actually suffering from a toxin overload that is produced by a particular strain of pathogenic bacteria. By clearing the treatable bacterial infections and utilizing various techniques to help reduce the toxin loads, there can be much improvement in the patient's overall condition.

Our Experience with Chronic Infections

Patients who have or who have had long term bacterial infections and who have taken antibiotics for extended periods may have serious damage to their immune systems, making them more susceptible to infection. Chronic infections are biofilms, they are colonies of a number of bacteria that together form colonies in various parts of the body - the sinuses, urinary tract, prostate and elsewhere that are inherently more resistant to antibiotics. While in-vitro lab tests may show sensitivity to various antibacterials, such infections typically do not respond to antibiotics. Dr. Tim Lu (MIT), a professor at MIT, explains why biofilms are antibiotic resistant, and why bacteriophage therapy can be effective:

Dr. Tim Lu - Biofilms and Phage Therapy

If you have dysbiosis and/or an infection that is caused by one of the treatable genuses (Staphylococcus spp., Streptococcus spp., Enterococcus spp., E. coli, Proteus spp., Pseudomonas aeruginosa, Salmonella spp., Shigella spp., Clostridium difficile (C.Diff), Klebsiella spp., Morganella spp. and several others) there is a good chance we can help - but NO GUARANTEE. You will need to test for the presence of these treatable pathogens and even if they are cleared, sometimes symptoms will persist.

Our Approach

Test to see if you have one of the treatable genuses of pathogenic bacteria. If you do, we can usually treat it and perhaps your symptoms will be reduced or eliminated. Based on our experience, it is common even for people who come to our clinic with ME/CFS to experience dramatic improvement after treating infections like E. coli. Indications that you may be a good candidate for phage therapy is intestinal disorders caused by bacterial infection or dysbiosis.


1 Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome
Ludovic Giloteaux(1), Julia K. Goodrich, (1,2), William A. Walters (1,2), Susan M. Levine (3), Ruth E. Ley (1,2) and Maureen R. Hanson (1*) Giloteaux et al. Microbiome (2016) 4:30 2 Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/ chronic fatigue syndrome
Dorottya Nagy-Szakal (1), Brent L. Williams (1), Nischay Mishra (1), Xiaoyu Che (1) Bohyun Lee (1), Lucinda Bateman (2), Nancy G. Klimas (3,9), Anthony L. Komaroff (4), Susan Levine (5), Jose G. Montoya (6), Daniel L. Peterson (7), Devi Ramanan (8), Komal Jain (1), Meredith L. Eddy (1), Mady Hornig (1), and W. Ian Lipkin (1*)

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