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ME/CFS is linked to microbiome changes

Updated: Jun 6, 2023

Exciting, robust research published this week links gut microbiome changes with ME/CFS, and suggests new avenues for diagnosis and treatment. 

IMAGES: visual abstracts and results from the studies linked below.

Two excellent studies show the microbiomes of patients with ME/CFS have important differences, including reduced diversity and a depletion in beneficial bacteria, especially those that produce anti-inflammatory butyrate (including Faecalibacterium and Roseburia). 

Differences in microbiome composition, function and interactions

One study compared the genetic makeup of the gut microbiomes of 106 people with ME/CFS with 91 healthy individuals. The results revealed important differences in microbiome diversity and quantity of gut bacteria as well as their metabolic pathways. 

Amazingly they also analysed interactions between species of gut bacteria and found key differences there too — indicating there is extensive reorganising of bacterial networks in ME/CFS.

Links to symptoms and severity

They also showed certain species are linked to symptoms and severity. For example, low Faecalibacterium was associated with greater fatigue. More research is needed to determine if differences in the gut microbiome are a consequence or cause of symptoms, but the researchers have strong hypotheses about how the links could be causal. 

Differences in the microbiomes of people at different stages in their illness

To look at microbiome changes at different stages of illness, the second study analysed clinical data, fecal samples, and blood samples from 149 people with ME/CFS who had been diagnosed within the previous four years (74 short-term) or who had been diagnosed more than 10 years ago (75 long-term) and 79 healthy controls.They found that individuals more newly diagnosed had more disrupted gut microbiome and marked reduction in butyrate producers. 

While the long-term ME/CFS patients had a more balanced microbiome (although still with notable differences) they had more severe symptoms and more significant changes in the *function* of bacteria, including tryptophan, butyrate, and propionic acid production, and anti-inflammatory betaine, sphingomyelin, serotonin, and cholesterol metabolism. 

The study was very thorough; ruling out other individual clinical and behavioural factors such as age, gender, IBS symptoms and lifestyle that could have accounted for these differences. 

Significantly, butyrate, tryptophan, and other microbial metabolites have been linked to gut immune regulation. Making links with other studies looking at the relationship between immune cells and the gut microbiome, the researchers propose how the microbiome might prime or sustain a disrupted immune response following illness onset.

These results are consistent with my experience in practice

The studies are consistent with what I’ve seen in my Microbiome Analysis practice, with people who have ME/CFS and Long Covid, in a number of ways. For example, those who have depleted populations of butyrate-producing bacteria, experience an improvement in fatigue and brain fog once Faecalibacterium has increased through targeted feeding with prebiotics. 

The researchers also found increased levels of nine species in ME/CFS, including Enterocloster bolteae and Ruminococcus gnavus, which are associated with autoimmune diseases and inflammatory bowel disease, respectively. They also noted the presence of species associated with IBS, including Bilophila and Escherichia, that I commonly find raised in results from clients with ME/CFS and Long Covid who have the gut symptoms that are so common with fatigue conditions. 

The two phenomenal studies were funded by the US National Institute for Health and have huge implications for the chronic fatigue community and the healthcare practitioners supporting them. 


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. DOI: 10.1016/j.chom.2023.01.004

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. DOI: 10.1016/j.chom.2023.01.001

Viola Sampson BSc MCMA is a registered Microbiome Analyst, Founder and Director of the Microbiome Group practice. You can book appointments with her team of Associates here. (Viola's availability is by waiting list only – currently at least 18 months' wait).

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