ArticleNature communications2023
Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 13 citations in OpenAlex.
- Growth Phase-Related DNA Methylation and Localized DNA Fragment Density Variation inEpigenomes · 2026Article
- MOSAIC enables selective transfer and fairness-aware generalization in cross-species DNA methylation prediction.Nucleic acids research · 2026Article
- Epigenetic Phase Variation in Bacterial Adaptation to Environmental Stress: A Narrative Review.Current microbiology · 2026Review
- Improved Cas9-targeted nanopore sequencing facilitates ultra-deep analysis of genomic variation.Cell reports methods · 2026Article
- Epigenetic regulation in prokaryotes: transcriptional and phenotypic outcomes of DNA methyltransferase activity.FEMS microbiology reviews · 2026Review
- MPore: database-driven identification of active methyltransferases in prokaryotic genomes from nanopore sequencing.Bioinformatics advances · 2026Article
- An open-source nanopore-only sequencing workflow for analysis of clonal outbreaks delivers short-read level accuracy.Journal of clinical microbiology · 2025Article
- Transcriptional diversification in a human-adapting zoonotic pathogen drives niche-specific evolution.Nature communications · 2025Article
- Detonating a "time bomb": how enteric infection stress triggers prophage induction in commensal microbiota and exacerbates disease progression.Frontiers in microbiology · 2025Review
- Nanopore sequencing of protozoa: Decoding biological information on a string of biochemical molecules into human-readable signals.Computational and structural biotechnology journal · 2025Article
- Review
- Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications.Genome research · 2024Article
- A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.Cell host & microbe · 2024Article
- Protective effect of synbiotic combination of Lactobacillus plantarum SC-5 and olive oil extract tyrosol in a murine model of ulcerative colitis.Journal of translational medicine · 2024Article
- A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
7 authors at 5 institutions in 2 countries.
Funding
Abstract
Three types of DNA methyl modifications have been detected in bacterial genomes, and mechanistic studies have demonstrated roles for DNA methylation in physiological functions ranging from phage defense to transcriptional control of virulence and host-pathogen interactions. Despite the ubiquity of methyltransferases and the immense variety of possible methylation patterns, epigenomic diversity remains unexplored for most bacterial species. Members of the Bacteroides fragilis group (BFG) reside in the human gastrointestinal tract as key players in symbiotic communities but also can establish anaerobic infections that are increasingly multi-drug resistant. In this work, we utilize long-read sequencing technologies to perform pangenomic (n = 383) and panepigenomic (n = 268) analysis of clinical BFG isolates cultured from infections seen at the NIH Clinical Center over four decades. Our analysis reveals that single BFG species harbor hundreds of DNA methylation motifs, with most individual motif combinations occurring uniquely in single isolates, implying immense unsampled methylation diversity within BFG epigenomes. Mining of BFG genomes identified more than 6000 methyltransferase genes, approximately 1000 of which were associated with intact prophages. Network analysis revealed substantial gene flow among disparate phage genomes, implying a role for genetic exchange between BFG phages as one of the ultimate sources driving BFG epigenome diversity.
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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.