The raw sequencing reads of a urinary metagenome sample was retrieved from GenBank (SRA Accession No. SRR19149281). This data represents DNA sequencing of a urine sample (sample ID 6162). In other words, both bacterial and viral constituents of the urinary microbiota are expected to be present. Details regarding the sample collection, DNA extraction, and sequencing was previously reported [51 ]. Briefly, a urine sample was obtained via transurethral catheterization of a female without lower urinary tract symptoms as part of a prior IRB-approved study (Loyola University Chicago, Maywood, IL, USA, IRB # 207102). A total of 10% by volume of AssayAssure® was added to 2 mL of the collected urine and stored at −80 °C. DNA was extracted from the thawed urine sample using the Norgen Urine DNA according to the manufacturer’s protocol with one exception: a starting volume of 500 uL was used and the binding solution was adjusted accordingly. The DNA sequenced at MIGS (Pittsburgh, PA, USA) using the Illumina DNA Prep kit and IDT 10 bp UDI indices on an Illumina NextSeq 2000 (paired-end reads, 2 × 151 bp). This raw data set includes human reads; the urine was not processed prior to DNA extraction to remove human cells (if present). We thus removed human reads from further analysis using Bowtie 2 v.2.4.5 and the application’s publicly available human genome index (GRCh38) [52 (link)]. Only reads that did not map to the human genome were considered further. This included 1,403,038 read pairs, 56.90% of the raw data. These filtered sequencing reads were assembled using metaSPAdes v.3.15.4 [53 (link)] with default parameters. Assembled contigs were then evaluated by VirSorter2 to identify putative viral sequences [31 (link)], the results of which were queried against the NCBI nr/nt nucleotide database via megaBLAST (using default parameters) to identify the most similar sequence record. The filtered reads and predicted viral sequences were next analyzed using PIE. Viral sequences exceeding the 99% threshold in PIE were queried against the NCBI nr/nt nucleotide database via BLAST in an effort to identify their putative taxonomy and annotated via the Bacteriophage “annotation recipe” on BV-BRC v.3.28.9 [54 (link)].
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