論文

国際誌
2021年1月4日

Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria.

Nature communications
  • Koji Yahara
  • ,
  • Masato Suzuki
  • ,
  • Aki Hirabayashi
  • ,
  • Wataru Suda
  • ,
  • Masahira Hattori
  • ,
  • Yutaka Suzuki
  • ,
  • Yusuke Okazaki

12
1
開始ページ
27
終了ページ
27
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1038/s41467-020-20199-9

Bacteriophages (phages), or bacterial viruses, are very diverse and highly abundant worldwide, including as a part of the human microbiomes. Although a few metagenomic studies have focused on oral phages, they relied on short-read sequencing. Here, we conduct a long-read metagenomic study of human saliva using PromethION. 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. Our analyses demonstrate enhanced scaffolding, and the ability to place a prophage in its host genomic context and enable its taxonomic classification. Our analyses also identify a Streptococcus phage/prophage group and nine jumbo phages/prophages. 86% of the phage/prophage group and 67% of the jumbo phages/prophages contain remote homologs of antimicrobial resistance genes. Pan-genome analysis of the phages/prophages reveals remarkable diversity, identifying 0.3% and 86.4% of the genes as core and singletons, respectively. Furthermore, our study suggests that oral phages present in human saliva are under selective pressure to escape CRISPR immunity. Our study demonstrates the power of long-read metagenomics utilizing PromethION in uncovering bacteriophages and their interaction with host bacteria.

リンク情報
DOI
https://doi.org/10.1038/s41467-020-20199-9
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/33397904
PubMed Central
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7782811

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