ArticleNature communications2019
Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 159 citations in OpenAlex.
- 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
- A genomic view of Earth's biomes.Nature reviews. Genetics · 2026Review
- Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota.Nature microbiology · 2025Article
- Nucleotide composition shapes gene expression inmSystems · 2025Article
- Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages.iScience · 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
- Matching excellence: Oxford Nanopore Technologies' rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content.Microbial genomics · 2024Article
- The elimination of two restriction enzyme genes allows for electroporation-based transformation and CRISPR-Cas9-based base editing in the non-competent Gram-negative bacteriumApplied and environmental microbiology · 2024Article
- Moving toward the Inclusion of Epigenomics in Bacterial Genome Evolution: Perspectives and Challenges.International journal of molecular sciences · 2024Review
- A sequential one-pot approach for rapid and convenient characterization of putative restriction-modification systems.mSystems · 2023Article
- Correcting modification-mediated errors in nanopore sequencing by nucleotide demodification and reference-based correction.Communications biology · 2023Article
- Extension of bacterial rDNA sequencing for simultaneous methylation detection and its application in microflora analysis.Scientific reports · 2023Article
- Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective.Nature medicine · 2023Review
- Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes.Science advances · 2023Article
- Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics.Microbiome · 2022Article
- Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes.mSystems · 2022Article
- Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity.The ISME journal · 2022Article
- NT-seq: a chemical-based sequencing method for genomic methylome profiling.Genome biology · 2022Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation plays important roles in prokaryotes, and their genomic landscapes-prokaryotic epigenomes-have recently begun to be disclosed. However, our knowledge of prokaryotic methylation systems is focused on those of culturable microbes, which are rare in nature. Here, we used single-molecule real-time and circular consensus sequencing techniques to reveal the 'metaepigenomes' of a microbial community in the largest lake in Japan, Lake Biwa. We reconstructed 19 draft genomes from diverse bacterial and archaeal groups, most of which are yet to be cultured. The analysis of DNA chemical modifications in those genomes revealed 22 methylated motifs, nine of which were novel. We identified methyltransferase genes likely responsible for methylation of the novel motifs, and confirmed the catalytic specificities of four of them via transformation experiments using synthetic genes. Our study highlights metaepigenomics as a powerful approach for identification of the vast unexplored variety of prokaryotic DNA methylation systems in nature.
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