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Chronic Fatigue Syndrome Has a Bacterial Signature

New studies find specific microbes are associated with ME/CFS.

Key points

  • Specific gut microbes are associated with ME/CFS.
  • The microbiota of ME/CFS patients is pro-inflammatory.
  • Chronic systemic inflammation may be at the root of ME/CFS.

“All disease begins in the gut” –Hippocrates

The microbiota is the community of bacteria, fungi, and viruses that calls the body home. The gut microbiota plays a pivotal role in health, and disruptions to it have been linked to a host of diseases, including myalgic encephalomyelitis/chronic disease syndrome (ME/CFS).

ME/CFS has been treated with skepticism for a long time by the medical world. It is not new; Charles Darwin and Florence Nightingale are thought to have suffered from it. In the past, when large-scale outbreaks occurred, they were often attributed to mass hysteria by certain doctors. That is, until those doctors themselves became sick. Recently, it has been taken more seriously, although there are still doubters.

The causes have been hard to pin down, but a virus has always been a top suspect. However, several viral options have been tested and mostly rejected, including polio, Epstein-Barr, and XMRV.

New Findings

Recently, two studies in Cell Host & Microbe found a bacterial linkage to ME/CFS. In the first study from Columbia University, Brent Williams, Ian Lipkin, and colleagues analyzed the gut bacteria in fecal samples from 106 people with ME/CFS and 91 healthy controls. They found key differences between the microbiota of ME/CFS patients and controls.

People with ME/CFS had a lower level of certain bacteria, such as Faecalibacterium prausnitzii, which produces butyrate – an important nutrient for the cells lining the gut. Butyrate provides over two-thirds of the gut’s energy requirements. Because it also moderates the immune system, F. prausnitzii helps to reduce inflammatory bowel disease and colon cancer.

Additionally, people with ME/CFS had a higher level of certain bacteria, such as Ruminococcus gnavus, which contributes to inflammation. Gut inflammation plays a major role in many chronic diseases because it can allow bacteria and toxins to enter the bloodstream, where they are pumped to every organ in the body.

The Columbia University results were buttressed by another study from Julia Oh, Derya Unutmaz, and colleagues at the Jackson Laboratory. They found reduced microbial diversity in people with ME/CFS and also found a similar reduction in F. prausnitzii.

In all, twelve species of bacteria were identified that were associated, both positively and negatively, with ME/CFS. The researchers say that these bacteria could be used as biomarkers, or signatures, for ME/CFS, potentially helping to diagnose the disease.

The exact role of the microbiota in ME/CFS is not yet fully known, and these studies show correlation, not causation. Still, it's not much of a stretch to think that inflammation may play a role in ME/CFS.

What Is ME/CFS?

ME/CFS is a complex illness characterized by extreme fatigue, sleep disturbances, cognitive difficulties, and a variety of other symptoms. The cause of ME/CFS is unknown, but it is thought to be triggered by a combination of factors, including genetics, infection, and environmental stressors.

Over a million people in the United States alone have ME/CFS. In 1969, it was inducted into the International Classification of Diseases (ICD) as myalgic encephalomyelitis. In 1996, it was renamed chronic fatigue syndrome and the two terms are now often merged as ME/CFS, although there is still some disagreement about whether it is one or two conditions. One of the nicknames for the disorder is "Raggedy Ann Syndrome," a colorful acknowledgment of the weakness noted by patients.

It is not a trivial disease. One patient said: “My personal experience of having ME/CFS feels like permanently having the flu, a hangover, and jet lag while being continually electrocuted (which means that pain plays at least as much of a role in my condition as fatigue).”

As well as physical symptoms, ME/CFS creates brain fog, depression, and anxiety, making it difficult to work, socialize, or attend school. ME/CFS sufferers also have another symptom, called post-exertional malaise (PEM), that causes them to suffer for days after physical exertion. All in all, it’s a lousy syndrome.

Sadly, a quarter of ME/CFS patients are completely house bound. Many suffer financially, as ME/CFS takes a toll on their ability to work and their need for extra medical care. Shockingly, some 50 percent of patients are unemployed or under-employed. ME/CFS patients lose an average of 65 days of work per year, ten times the average patient rate.

Not everyone is happy with the CFS designation, since “chronic fatigue” sounds trivial to them, and makes many clinicians suspect patients are simply malingerers. If you show up with symptoms of ME/CFS, you may find your doctor saying, “Yeah, I feel tired too.” This dismissive attitude is why many sufferers hide their symptoms and try to muddle through on their own.

According to another patient, “I believe that the words ‘Chronic Fatigue’ are the kiss of death. Who in this overwrought, stress-driven society isn't ‘fatigued’ a good deal of the time? What people don't get is that this fatigue for people like me keeps me in bed for days at a time and prevents me from doing everyday errands and even simple house tasks on some days.”

There are a few things that people with ME/CFS can do to improve their microbiota. These include:

  • Eat a healthy diet that is rich in fiber (prebiotics) and probiotics.
  • Avoid antibiotics, if possible.
  • Get sufficient sleep on a regular basis.

These changes will help to improve the health of the microbiota and may reduce the symptoms of ME/CFS. More studies are needed, but this research is a wonderful start for the millions of sufferers who are finally being heard.


Guo, et al. Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS. Cell Host & Microbe, February 8, 2023.

Xiong, et al. Multi-‘omics of host-microbiome interactions in short- and long-term Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). Cell Host & Microbe, February 8, 2023.

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