ArticleMicrobiome2022
Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics.
Article in Microbiome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Long-read metagenomics and methylation-based binning support the discovery of antibiotic resistance gene-host associations in complex communities.Genome biology · 2026Article
- Community structure and methylation of microbes in an artificially forced sediment core.Microbiology spectrum · 2026Article
- Environmental disturbances and cyanobacterial traits shape prokaryotic dynamics in a eutrophic Mediterranean coastal lagoon.Environmental microbiome · 2026Article
- Marine BacteriumJournal of natural products · 2026Article
- Viromics approaches for the study of viral diversity and ecology in microbiomes.Nature reviews. Genetics · 2026Review
- Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.Nucleic acids research · 2025Article
- Multiple roles of DNA methylation in sea-ice bacterial communities and associated viruses.The ISME journal · 2025Article
- Understanding prokaryotic adaptation through advanced DNA methylation detection techniques.The ISME journal · 2025Review
- The ageing virus hypothesis: Epigenetic ageing beyond the Tree of Life.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Interplay of intracellular and trans-cellular DNA methylation in natural archaeal consortia.Environmental microbiology reports · 2024Article
- Antarctic lake viromes reveal potential virus associated influences on nutrient cycling in ice-covered lakes.Frontiers in microbiology · 2024Article
- PacBio sequencing of human fecal samples uncovers the DNA methylation landscape of 22 673 gut phages.Nucleic acids research · 2023Article
- Dual thermal ecotypes coexist within a nearly genetically identical population of the unicellular marine cyanobacteriumProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species.The ISME journal · 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
- The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms.International journal of molecular sciences · 2023Review
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life.
resultsWe reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark.
conclusionsOverall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome. Video Abstract.
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