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

Koji Yahara (), Masato Suzuki, Aki Hirabayashi, Wataru Suda, Masahira Hattori, Yutaka Suzuki and Yusuke Okazaki
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Koji Yahara: National Institute of Infectious Diseases
Masato Suzuki: National Institute of Infectious Diseases
Aki Hirabayashi: National Institute of Infectious Diseases
Wataru Suda: RIKEN Center for Integrative Medical Sciences
Masahira Hattori: RIKEN Center for Integrative Medical Sciences
Yutaka Suzuki: The University of Tokyo
Yusuke Okazaki: National Institute of Advanced Industrial Science and Technology

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: Abstract 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.

Date: 2021
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DOI: 10.1038/s41467-020-20199-9

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