Metagenomics does not detect differences in microbial DNA content in the plasma of ME/CFS patients compared to controls

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating disease causing indefinite fatigue. ME/CFS has long been hypothesised to have an infectious cause; however, no specific infectious agent has been identified. We used metagenomics to analyse plasma samples from individuals with ME/CFS and compare their microbial content to technical controls as well as three control groups: individuals with alternatively diagnosed chronic Lyme syndrome, systemic lupus erythematosus, and healthy controls. We found very low microbial content in the plasma, and the few differences in bacterial or viral abundance we observed between study groups were more likely caused by contamination and batch effects due to processing of samples in groups. Our results highlight the importance of including negative controls in all metagenomic analyses. Many of the taxonomic groups we saw in our plasma-free negative control samples have previously been associated with diseases, including ME/CFS, demonstrating how incorrect conclusions may arise if controls are not used and batch effects not accounted for. While our study does not rule out an infectious cause for ME/CFS, it calls into question the validity of some results published using less controlled metagenomic approaches.