2.3. DNA Sequencing and Analysis of VA7 Genome

Phage VA7 DNA was extracted from a high-titer phage stock, as described previously [25]. Subsequently, its genome was sequenced using an Illumina MiSeq device (Illumina, San Diego, CA, USA) at the VIB Nucleomics Core (Leuven, Belgium). After sequencing, the raw reads were trimmed (Trimmomatic) and assembled (SPAdes) in one contig [26,27]. Using MEGA X [28], the assembled phage genome was aligned to the closest characterized phage as identified by BLASTn [29] and a ViPTree [30] analysis (Bacteroides phage B124-14; {"type":"entrez-nucleotide","attrs":{"text":"NC_016770","term_id":"374671600","term_text":"NC_016770"}}NC_016770). The phage’s taxonomy was further delineated using VIRIDIC [31], which calculates the virus intergenomic distance. Next, the VA7 genome was annotated using RASTtk [32] and manually curated by BLASTp. tRNAs were identified with tRNAscan-SE v2.0. [33,34]. Finally, the phage genome was visualized using EasyFig [34].