Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects.
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 the RNA from plasma samples from 25 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 (N = 13), systemic lupus erythematosus (N = 11), and healthy controls (N = 25). We found that the majority of sequencing reads were removed during host subtraction, thus there was very low microbial RNA content in the plasma. The effects of sample batching and contamination during sample processing proved to outweigh the effects of study group on microbial RNA content, as the few differences in bacterial or viral RNA abundance we did observe between study groups were most likely caused by contamination and batch effects. Our results highlight the importance of including negative controls in all metagenomic analyses, since there was considerable overlap between bacterial content identified in study samples and control samples. For example, Proteobacteria, Firmicutes, Actinobacteria, and Bacteriodes were found in both study samples and plasma-free negative controls. 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.
School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada.
Ruth R
RR
Miller
British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada.
Miguel
M
Uyaguari-Diaz
British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada.
Mark N
MN
McCabe
British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada.
Vincent
V
Montoya
School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada.|British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada.
Jennifer L
JL
Gardy
Centre for Health Evaluation and Outcome Sciences, Vancouver, British Columbia, Canada.
Shoshana
S
Parker
Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
Theodore
T
Steiner
British Columbia Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada.|Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
William
W
Hsiao
Coastal Genomics Inc., Burnaby, British Columbia, Canada.
Matthew J
MJ
Nesbitt
Department of Pathology, Sidra Medical and Research Center, Doha, Qatar.
Patrick
P
Tang
School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada.|British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada.
David M
DM
Patrick
D000328:Adult; D000368:Aged; D059018:DNA Contamination; D003937:Diagnosis, Differential; D015673:Fatigue Syndrome, Chronic / Q000378:metabolism*; D005260:Female; D006801:Humans; D008180:Lupus Erythematosus, Systemic / Q000382:microbiology; D008193:Lyme Disease / Q000382:microbiology; D008297:Male; D056186:Metagenomics / Q000379:methods*; D008875:Middle Aged; D010802:Phylogeny; D012329:RNA, Bacterial / Q000097:blood*; D012367:RNA, Viral / Q000097:blood*; D017423:Sequence Analysis, RNA / Q000379:methods*; D055815:Young Adult
D012329:RNA, Bacterial; D012367:RNA, Viral