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

Abstract

Background: 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).

Results: 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 %.

Conclusions: 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.

Keywords: Beta-diversity; Chronic fatigue syndrome; Inflammation; Lipopolysaccharides; Microbial translocation; Microbiome; Myalgic encephalomyelitis.

Fig. 1

Microbial translocation, gastrointestinal tract damage, and evidence for direct LPS stimulation in vivo in ME/CFS: plasma levels of hsCRP (a), LPS (b), I-FABP (c), sCD14 (d), and LBP (e) determined in our cohorts of controls and ME/CFS diagnosed individuals. p values were calculated by the Wilcoxon-Mann-Whitney U test

Fig. 2

Correlation between plasma levels of LPS and sCD14 (a), plasma levels of LPS and LBP (b), plasma levels of sCD14 and LBP (c), and plasma levels of hsCRP and sCD14 (d) in the ME/CFS population. Spearman’s rank test was used to determine correlations

Fig. 3

Rarefaction curves and confusion matrix. a Rarefaction curves for the microbiota of healthy individuals and ME/CFS patients (each group was rarefied to the number of sequences of the less-sequenced sample, i.e., 32223 sequences). The p value was calculated by the Wilcoxon rank-sum test and b comparison of alpha diversity indexes in ME/CFS and healthy individuals

Fig. 4

Composition of the gut microbiome of healthy individuals and ME/CFS patients. Relative abundance of phylum-level (a) and family-level (b) gut microbial taxa

Fig. 5

Histogram of the LDA scores computed for genera differentially abundant between ME/CFS and healthy individuals. ME/CFS-enriched genera are indicated with a positive LDA score, and genera enriched in healthy individuals have a negative score. The LDA score indicates the effect size and ranking of each differentially abundant taxon

Fig 6

Receiver operating characteristic curves (a) for controls and ME/CFS patients determined using the inflammatory markers and sequencing datasets (even sampled at 32,233 sequences) and a supervised learning approach with randomForest algorithm and (b) confusion matrix for random forest analysis (values are presented as percentage) and ROC area under the curve (AUC) value for 97 % OTUs collapsed at the genus level. Mean AUC ROC value for five times repeated, 10-fold cross validation