Attempts have also been made to explore the associations between human gut virome alterations and diseases 7, 9, 10. For example, there have been more attempts to characterize “healthy gut phageome” since a study in 2016 conducted deep-sequencing of DNA from virus-like particles and revealed the presence of completely assembled phage genomes in 64 healthy individuals around the world 8. With the rise of next-generation metagenome sequencing technologies, human gut virome studies have increased rapidly 7. Among them, bacteriophages (phages), or bacterial viruses, in the intestinal microbiome have received increasing attention over the last decade 5, 6, whereas those present in the oral microbiota have been less studied. The two most diverse human microbiomes are intestinal and oral microbiota, which harbor hundreds of coexisting species, including bacteria and viruses. Interspecies networks within the microbiome can modulate energy metabolism pathways and affect human health. Human microbiomes are of enormous interest to researchers 1, 2 and have been model systems for studying polymicrobial communities 3, 4. Our study demonstrates the power of long-read metagenomics utilizing PromethION in uncovering bacteriophages and their interaction with host bacteria.
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.
0 kommentar(er)
