ArticleNucleic acids research2020
Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 26 citations in OpenAlex.
- TPMM: three-component posterior mixture model enables robust inverton detection in low-depth metagenomes and suggests potential viral invertons.Bioinformatics (Oxford, England) · 2026Article
- Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.Cell host & microbe · 2026Article
- Evolutionary Genomics of Human Gut Bacteria: Ecological Plasticity Across the Mutualism-Pathogenicity Spectrum.International journal of molecular sciences · 2026Review
- Phase variation inEngineering microbiology · 2026Article
- Gene regulation inMicrobiology and molecular biology reviews : MMBR · 2025Review
- Bacteriophage-driven DNA inversions shape bacterial functionality and long-term co-existence inGut microbes · 2025Article
- Lessons from the model gut BacteroidalesJournal of bacteriology · 2025Review
- Carbohydrates and the oxidative branch of the pentose phosphate pathway modifyJournal of bacteriology · 2025Article
- Dietary carbohydrates alter immune-modulatory functionalities and DNA inversions in Bacteroides thetaiotaomicron.Nature communications · 2025Article
- Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages.iScience · 2025Article
- Genomic alterations in Bacteroides fragilis favor adaptation in colorectal cancer microenvironment.BMC genomics · 2025Article
- Combinatorial phenotypic landscape enables bacterial resistance to phage infection.bioRxiv : the preprint server for biology · 2025Article
- Generation of tools for expression and purification of the phage-encoded Type I restriction enzyme inhibitor, Ocr.Microbiology (Reading, England) · 2024Article
- Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota.Cell host & microbe · 2024Article
- Article
- CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei.Nature communications · 2024Article
- Systematic identification of gene-altering programmed inversions across the bacterial domain.Nucleic acids research · 2023Article
- Small RNAs Go Global in Human GutJournal of bacteriology · 2021Article
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Authors and funding
13 authors at 7 institutions in 4 countries.
Funding
Abstract
The genomes of gut Bacteroidales contain numerous invertible regions, many of which contain promoters that dictate phase-variable synthesis of surface molecules such as polysaccharides, fimbriae, and outer surface proteins. Here, we characterize a different type of phase-variable system of Bacteroides fragilis, a Type I restriction modification system (R-M). We show that reversible DNA inversions within this R-M locus leads to the generation of eight specificity proteins with distinct recognition sites. In vitro grown bacteria have a different proportion of specificity gene combinations at the expression locus than bacteria isolated from the mammalian gut. By creating mutants, each able to produce only one specificity protein from this region, we identified the R-M recognition sites of four of these S-proteins using SMRT sequencing. Transcriptome analysis revealed that the locked specificity mutants, whether grown in vitro or isolated from the mammalian gut, have distinct transcriptional profiles, likely creating different phenotypes, one of which was confirmed. Genomic analyses of diverse strains of Bacteroidetes from both host-associated and environmental sources reveal the ubiquity of phase-variable R-M systems in this phylum.
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