Researchers from New York recently published an amazing study in the journal Microbiome.1 With 48 ME/CFS patients and 39 controls a sophisticated technique (sequencing ribosomal RNA genes) was performed to comprehensively profile the bacteria within stool samples. Five different blood inflammatory markers were also measured. A number of key findings are as follows.

Firstly as a group all five inflammatory markers were higher than controls:

  • C-reactive protein (CRP) – general inflammation marker.
  • Intestinal fatty acid-binding protein (I-FABP) – marker for gastrointestinal tract damage.
  • Lipopolysaccharide (LPS) – an endotoxin produced from certain intestinal bacteria.
  • LPS-binding protein (LBP) – indicator of LPS stimulation.
  • Soluble CD14 (sCD14) – indicator of LPS stimulation.

The finding of elevated LPS and also elevated levels of markers indicating increased LPS levels is striking as LPS is a potent inflammation inducer. Elevated LPS levels indicate increased levels of intestinal LPS-producing bacteria and subsequent absorption of LPS and inflammation.

Furthermore stool bacterial levels in ME/CFS patients compared to healthy controls was distinctly different. Firstly the total bacterial diversity was low in ME/CFS patients. Increased diversity is generally considered a sign of a healthy microbiome. Secondly a few dozen bacteria were either specifically elevated or depressed in ME/CFS patients as compared to controls. In the image below the bacteria next to the purple bars were higher in ME/CFS patients and the bacteria next to the red bars were higher in healthy controls.

Gut and CFS

Another striking finding of this study is using a computer analysis based on the blood and stool markers, an individuals test results could be correctly predicted as either a control or ME/CFS result with an accuracy of 82.93%.

This study clearly demonstrates an abnormal intestinal microbiome in ME/CFS patients and suggests it’s associated with systemic inflammation. Research in this area is still in its infancy. Systematic inflammation however also affects the intestinal microbiome. Inflammation influences the terrain of the gut which causes an alteration of microbial balance. The findings of this study are likely bidirectional. An unhealthy microbiome triggers systemic inflammation and systemic inflammation from other sources alters the microbiome.

Either way it seems prudent to pay attention to this issue and to do what can be done to encourage a healthy microbiome. Microbiome modification through diet, prebiotics, probiotics, antimicrobial agents and correction of factors causing systemic inflammation will likely prove beneficial to at least some patients. The diet most beneficial for the intestinal microbiome is one which is predominantly whole plant foods.


  1. Giloteaux L, Goodrich JK1, Walters WA1, Levine SM, Ley RE1, Hanson MR. Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome. Microbiome. 2016 Jun 23;4(1):30. doi: 10.1186/s40168-016-0171-4.