MEA research assistant Sophie Loup discusses the latest major microbiome study | 1 July 2016

July 1, 2016

From Microbiome, 23 June 2016.

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

Ludovic Giloteaux, Julia K. Goodrich, William A. Walters, Susan M. Levine, Ruth E. Ley and Maureen R. Hanson
1) Department of Molecular Biology and Genetics, Cornell University
2) Department of Microbiology, Cornell University
3) Private Practice


Gastrointestinal disturbances are among symptoms commonly reported by individuals diagnosed with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). However, whether ME/CFS is associated with an altered microbiome has remained uncertain. Here, we profiled gut microbial diversity by sequencing 16S ribosomal ribonucleic acid (rRNA) genes from stool as well as inflammatory markers from serum for cases (n = 48) and controls (n = 39). We also examined a set of inflammatory markers in blood: C-reactive protein (CRP), intestinal fatty acid-binding protein (I-FABP), lipopolysaccharide (LPS), LPS-binding protein (LBP), and soluble CD14 (sCD14).


We observed elevated levels of some blood markers for microbial translocation in ME/CFS patients; levels of LPS, LBP, and sCD14 were elevated in ME/CFS subjects. Levels of LBP correlated with LPS and sCD14 and LPS levels correlated with sCD14. Through deep sequencing of bacterial rRNA markers, we identified differences between the gut microbiomes of healthy individuals and patients with ME/CFS. We observed that bacterial diversity was decreased in the ME/CFS specimens compared to controls, in particular, a reduction in the relative abundance and diversity of members belonging to the Firmicutes phylum. In the patient cohort, we find less diversity as well as increases in specific species often reported to be pro-inflammatory species and reduction in species frequently described as anti-inflammatory. Using a machine learning approach trained on the data obtained from 16S rRNA and inflammatory markers, individuals were classified correctly as ME/CFS with a cross-validation accuracy of 82.93 %.


Our results indicate dysbiosis of the gut microbiota in this disease and further suggest an increased incidence of microbial translocation, which may play a role in inflammatory symptoms in ME/CFS.


This study adds interesting findings to the growing body of research on the link between ME/CFS and the gut.

In this study, the bacteria present in the gut of ME/CFS patients were less diverse than in controls.

There was also evidence suggesting that the gastrointestinal track of ME/CFS patients is more of a pro-inflammatory environment than in controls, which could explain their findings of more microbial translocation occurring in patients.

The findings could explain some of the symptoms of ME/CFS, and they offer an interesting area of further research for treatment.

Treatment by probiotics is however premature, and we do not recommend that patients purchase them in our current state of knowledge.

Finally, the researchers were able to correctly diagnose 82% of ME/CFS participants through stool samples and blood work, which is an important step towards the development of a biomarker test for the disease.

Lay summary

There is growing interest in the role of the gut microbiome in ME/CFS. The Invest in ME conference in early June this year saw several interesting presentations on the subject, including one by Maureen Hanson who is part of the team that conducted the present study. See here for a report on the conference by our medical adviser, Dr Charles Shepherd. We also have a lay summary of another recently published study on the changes in the gut and blood of ME/CFS patients following exercise available here.

ME/CFS sufferers often report gastrointestinal problems. The present study aims to assess whether the gut microbiota (or microbiome) differs between ME/CFS patients and controls. The gut microbiota is the name given to the microorganisms in our intestines. It plays an important role in the protection against infections. Disturbances in the gut microbiota have been implicated in obesity, type 2 diabetes and inflammatory bowel disease. The gut microbiota is influenced by our diet, our health, our age and our genetic make-up.

To identify the microorganisms present in the gut of ME/CFS patients (49 people) and controls (39 people), the study sequenced 16S ribosomal ribonucleic acid (rRNA) genes from stool. 16S rRNA sequencing is a cheap and fast way to identify which bacteria are present in a sample. The study also looked at inflammatory markers from serum and blood. In the blood, it looked at C-reactive protein (CRP), intestinal fatty acid-binding protein (I-FABP), lipopolysaccharide (LPS), LPS-binding protein (LBP) and soluble CD14 (sCD14).
· CRP measures general levels of inflammation in the body.
· I-FABP was used as a marker for gastrointestinal tract integrity.
· LPS is part of certain bacteria and leads to negative effects on human health, especially in high doses where it can lead to shock. It is a marker of microbial translocation, which is the passage of microbes from the gastrointestinal tract to other parts of the body, such as organs and the blood. Microbial translocation can lead to abnormal immune activation.
· LBP is produced by the body most probably to deal with the presence of LPS.
· sCD14 detects LPS through LBP.

Levels of CRP were higher in the ME/CFS group than in the control group, but the difference between the two was not statistically significant, which means we cannot rule out that it was due to chance. Levels of LPS, LBP and sCD14 were elevated in ME/CFS patients when compared to controls. Levels of LBP correlated with LPS and sCD14, and LPS levels correlated with sCD14. This suggests that more microbial translocation occurs in people affected by ME/CFS than in controls.

The microbiota in the stool of ME/CFS patients differed from that of controls, but no single precise alteration in the gut microbiota of all ME/CFS patients in the study was found. At the family and phylum levels (levels in the hierarchy used to classify bacteria), the differences were not significant. However, at the operational taxonomic unit (OTU) level, 40 OTUs were found to be significantly different between groups. This means the differences in terms of OTUs between ME/CFS patients and controls are very unlikely to be due to chance. OTUs are operational definitions used to classify similar items; here they are used to classify bacteria. In this study, bacteria that were 97% similar in their 16S rRNA genes were classified together.

Bacterial diversity was decreased in the ME/CFS group. In particular, the abundance and diversity of bacteria belonging to the Firmicutes phylum was lower, which has also been noted in Crohn’s disease patients. In the ME/CFS group, there was also an increase of bacteria species often reported to be pro-inflammatory and a decrease of species often reported as anti-inflammatory.

This suggests that the gastrointestinal tract of ME/CFS patients is a pro-inflammatory environment, which could lead to microbial translocation and an immune response, and could explain some of the symptoms of ME/CFS. At the moment, it is not possible to say whether this altered gut microbiota is a cause or a consequence of ME/CFS. However, these findings suggest treatments could be targeted at the gastrointestinal tract to improve symptoms.

Using a machine learning approach (where the computer comes up with its own classification programme based on the cases provided), the study was able to classify correctly 82% of patients as having ME/CFS using their stool and blood samples. This approach could therefore be a complement to other diagnoses or used as an initial diagnosis. It is an important step in the development of a biomarker test. A larger sample is required first to check that the classification remains accurate when applied to a greater number of patients.

So should we all take probiotics to improve our symptoms now? Not so fast! There are many different probiotics available, and research is not able to say yet which type will work for ME/CFS. Furthermore, probiotics are classified as food rather than medicine, and therefore do not undergo the rigorous testing that medicines do. This means that we can’t be sure that the products we buy actually contain the bacteria stated on the label and that the bacteria can survive long enough to reach the gut. There is likely to be a huge difference between the probiotics used in clinical trials and the supplements sold in shops. What is more, there have been reports linking probiotics to severe side effects in people with serious underlying medical problems, and many research studies on probiotics have not looked closely at safety. Probiotics cannot be recommended yet as treatment for ME/CFS.

See and for more information on probiotics.

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