ArticleAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2023
Long-Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage-Encoded Methyltransferases.
Article in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 24 citations in OpenAlex.
- Alternating High-Fat and Polysaccharide Diets Modulates Gut Phage-Bacterial Interplay.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Single cell viral tagging ofGut microbes · 2025Article
- LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation.Nature communications · 2025Article
- Unlocking the genomic repertoire of a cultivated megaphage.Npj viruses · 2025Article
- Review
- Virological and Pharmaceutical Properties of Clinically Relevant Phages.Antibiotics (Basel, Switzerland) · 2025Article
- Article
- Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages.iScience · 2025Article
- Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks.Virus research · 2025Article
- Multiple roles of DNA methylation in sea-ice bacterial communities and associated viruses.The ISME journal · 2025Article
- Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data.Bioinformatics advances · 2025Article
- phage therapy candidates from Sphae: An automated toolkit for predicting sequencing data.bioRxiv : the preprint server for biology · 2024Article
- Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.Science advances · 2024Article
- Isolation and Characterization of Six NovelPHAGE (New Rochelle, N.Y.) · 2024Article
- Efficient Recovery of Complete Gut Viral Genomes by Combined Short- and Long-Read Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Review
- PacBio sequencing of human fecal samples uncovers the DNA methylation landscape of 22 673 gut phages.Nucleic acids research · 2023Article
- Long-Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage-Encoded Methyltransferases.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 7 institutions in 3 countries.
Funding
Abstract
DNA methylation plays a crucial role in the survival of bacteriophages (phages), yet the understanding of their genome methylation remains limited. In this study, DNA methylation patterns are analyzed in 8848 metagenome-assembled high-quality phages from 104 fecal samples using single-molecule real-time sequencing. The results demonstrate that 97.60% of gut phages exhibit methylation, with certain factors correlating with methylation densities. Phages with higher methylation densities appear to have potential viability advantages. Strikingly, more than one-third of the phages possess their own DNA methyltransferases (MTases). Increased MTase copies are associated with higher genome methylation densities, specific methylation motifs, and elevated prevalence of certain phage groups. Notably, the majority of these MTases share close homology with those encoded by gut bacteria, suggesting their exchange during phage-bacterium interactions. Furthermore, these MTases can be employed to accurately predict phage-host relationships. Overall, the findings indicate the widespread utilization of DNA methylation by gut DNA phages as an evasion mechanism against host defense systems, with a substantial contribution from phage-encoded MTases.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.