Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues

Baldwin, Don A.; Feldman, Michael; Alwine, James C.; Robertson, Erle S.

PCR amplification using universal 16S rRNA primers, followed by amplicon sequencing, is the most widely used strategy for exploring investigations in associated microbiomes and provides an effective discovery tool (17) . However, this will work only for bacterial species with amplicons that survive population PCR but not for viruses or eukaryotic microorganisms. 16S rRNA sequencing can also be used to screen large sets of samples but may have difficulty in discriminating between strains or reporting the presence of genomic variants or pathogenicity factors. Deep sequencing of the total DNA from a sample can certainly identify bacterial, viral, and other microbiome members (3, 17, 18) but with a severe penalty in efficiency. Even if the field attains the as-yet-unrealized goal of a cost of $1,000 per genome, total DNA sequencing will be an expensive method for screening hundreds or thousands of experimental and control samples to detect associations of pathogens with a particular disease. Depending on the specimen sampled, the data may overwhelmingly be from host human sequences, creating an unnecessarily large search space for locating pathogen signatures and resulting in the majority of sequence reads being discarded.