Furthermore, our study suggests that oral phages present in human saliva are under selective pressure to escape CRISPR immunity. Pan-genome analysis of the phages/prophages reveals remarkable diversity, identifying 0.3% and 86.4% of the genes as core and singletons, respectively. 86% of the phage/prophage group and 67% of the jumbo phages/prophages contain remote homologs of antimicrobial resistance genes. Our analyses also identify a Streptococcus phage/prophage group and nine jumbo phages/prophages. Our analyses demonstrate enhanced scaffolding, and the ability to place a prophage in its host genomic context and enable its taxonomic classification. Our analyses, which integrate both PromethION and HiSeq data of >30 Gb per sample with low human DNA contamination, identify hundreds of viral contigs 0–43.8% and 12.5–56.3% of the confidently predicted phages and prophages, respectively, do not cluster with those reported previously. Here, we conduct a long-read metagenomic study of human saliva using PromethION. Although a few metagenomic studies have focused on oral phages, they relied on short-read sequencing. Bacteriophages (phages), or bacterial viruses, are very diverse and highly abundant worldwide, including as a part of the human microbiomes.
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