Shotgun Metagenome Sequencing of Rectal Swab Samples from Cervical Cancer Patients

Forty-one patients admitted to the University of Texas, M.D. Anderson Cancer Center with diagnosis cervical cancer participated in the study. The patients were enrolled on an Institutional Review Board (IRB) approved protocol. Informed consent was obtained to collect rectal swabs. All patient samples were acquired prior to receiving any treatment. Samples were collected from each out of 41 patients by a clinician performing rectal exams using a matrix-designed quick-release Isohelix swab. The swabs were initially stored in proteinase K and lysis buffer (Isohelix) within 1 h of sample collection and then were frozen and kept at -80C. Whole Genome Shotgun sequencing was performed on genomic bacterial DNA (gDNA), which was extracted to maximize bacterial DNA yield from specimens while keeping background amplification to a minimum. Libraries were constructed from each sample using the KAPA Hyper Prep Kit (Kapa Biosystems, Wilmington, MA, USA) and sequenced using the Illumina HiSeqX platform with the 2 x 150 bp paired-end read protocol.