Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating disease causing profound unexplained fatigue in over 400,000 Canadians, yet its etiology is unknown. It has long been hypothesized that ME/CFS may have infectious origins, however, no causal agent has been confirmed. We conducted a metagenomic case-control study to compare the microbial content of plasma in individuals with ME/CFS to healthy controls, as well as a subset of controls with systemic lupus erythematosus (SLE). Such an approach may enable the association of novel microbes, not previously hypothesized to have a role in ME/CFS to be associated with the disease.
We sequenced plasma samples from 14 patients with ME/CFS, 14 healthy controls and 11 controls with SLE on the Illumina HiSeq at least once, as well as 6 negative water controls, resulting in a mean of 13,000,000 read pairs per sample. After filtering to remove low quality and non-specific reads, as well as host contamination, a mean of 160,000 reads per sample remained. These were assigned to genera and phyla using RAPSearch and MEGAN4.
The most common bacterial genera found were Helicobacter, Escherichia and Pseudomonas, of which particularly Pseudomonas was also highly abundant in the negative controls (Fig 1). After accounting for contamination and sequencing batch effects no differences were found between viruses or bacteria from each study group, with only the negative controls appearing different (Fig 2). There was also no difference in Simpson or Shannon diversity between groups.
Our preliminary investigation has been unable to find any microbial associations with ME/CFS. When performing metagenomic analyses, great care must be taken to control for contamination and batch-to-batch differences in both DNA extraction and library preparation, including use of negative controls. This study provides an initial signal that ME/CFS may not have a microbial cause, however, further experiments, perhaps using other sample types, are required to confirm the findings.
S. Parker, None
T. Steiner, None
V. Montoya, None
P. Tang, None
D. M. Patrick, None