ArticleNature communications2021
Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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51 citing papers in PubMed, 82 citations in OpenAlex.
- Longitudinal development of infant oral ecosystem: salivary metabolomic, bacteriome, and virome dynamics in early infancy.mSystems · 2026Article
- The Oral Virome in Dental Caries: From Ecological Disruptors to Therapeutic Opportunities.Journal of microbiology and biotechnology · 2026Review
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- Shotgun metagenomic analysis of the oral microbiomes of children with noma.PLoS neglected tropical diseases · 2026Article
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- Host-pathogen interactions in periodontitis: an integrative interkingdom perspective.Frontiers in immunology · 2026Review
- A comparison of methods for the optimal recovery of the human fecal virome.ISME communications · 2026Article
- The potential of mRNA markers in body fluids and personal source analysis based on the QNome nanopore sequencing.International journal of legal medicine · 2026Article
- Ecology of prokaryotic DNA viruses in a highly impacted coastal lagoon revealed through comparative and temporal metagenomics.ISME communications · 2026Article
- Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations.NAR genomics and bioinformatics · 2025Article
- Detection ofFood chemistry. Molecular sciences · 2025Article
- Comparing Genome Sequencing Methods to Reconstruct the Spread of Piscine Myocarditis Virus in Ireland.Journal of fish diseases · 2025Article
- Article
- Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome.Briefings in bioinformatics · 2024Article
- 4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs.Nucleic acids research · 2024Article
- Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system.Microbiome · 2024Article
- The oral microbiome: diversity, biogeography and human health.Nature reviews. Microbiology · 2024Review
- The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies.Microbial genomics · 2024Article
- Findings and methodologies in oral phageome research: a systematic review.Journal of oral microbiology · 2024Review
- Shotgun metagenomic analysis of saliva microbiome suggests Mogibacterium as a factor associated with chronic bacterial osteomyelitis.PloS one · 2024Article
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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