ArticleNucleic acids research2018
Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 52 citations in OpenAlex.
- A CRISPRi Gene Regulation System for Bifidobacteria.Microbial biotechnology · 2025Article
- Advances in Diversity, Evolutionary Dynamics and Biotechnological Potential of Restriction-Modification Systems.Microorganisms · 2025Review
- Highly efficient CRISPR-Cas9 base editing inApplied and environmental microbiology · 2025Article
- Moving toward the Inclusion of Epigenomics in Bacterial Genome Evolution: Perspectives and Challenges.International journal of molecular sciences · 2024Review
- Harnessing the endogenous Type I-C CRISPR-Cas system for genome editing inApplied and environmental microbiology · 2024Article
- Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group.Nature communications · 2023Article
- Establishment of CRISPR-Cas9 system in Bifidobacteria animalis AR668.Microbial cell factories · 2023Article
- HMO-primed bifidobacteria exhibit enhanced ability to adhere to intestinal epithelial cells.Frontiers in microbiology · 2023Article
- Biotechnological Applications of Probiotics: A Multifarious Weapon to Disease and Metabolic Abnormality.Probiotics and antimicrobial proteins · 2022Review
- Genomic and epigenetic landscapes drive CRISPR-based genome editing inProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Characterization of CRISPR-Cas systems inMicrobial genomics · 2022Article
- Precision Methylome and In Vivo Methylation Kinetics Characterization of Klebsiella pneumoniae.Genomics, proteomics & bioinformatics · 2022Article
- Genomic Features and Pervasive Negative Selection inMicrobiology spectrum · 2022Article
- A Proposed Framework to Identify Dispensable and Essential Functions in Bifidobacteria: Case Study of Bifidobacterium breve UCC2003 as a Prototype of Its Genus.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Changes in the genomes and methylomes of threeFrontiers in microbiology · 2022Article
- Diversity of Human-Associated Bifidobacterial Prophage Sequences.Microorganisms · 2021Article
- Comparative Genomic Analysis ofGenes · 2021Article
- Molecular analysis of the replication functions of the bifidobacterial conjugative megaplasmid pMP7017.Microbial biotechnology · 2021Article
- Broad Purpose Vector for Site-Directed Insertional Mutagenesis inFrontiers in microbiology · 2021Article
- A Resource for Cloning and Expression Vectors Designed for Bifidobacteria: Overview of Available Tools and Biotechnological Applications.Methods in molecular biology (Clifton, N.J.) · 2021Review
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bifidobacterium breve represents one of the most abundant bifidobacterial species in the gastro-intestinal tract of breast-fed infants, where their presence is believed to exert beneficial effects. In the present study whole genome sequencing, employing the PacBio Single Molecule, Real-Time (SMRT) sequencing platform, combined with comparative genome analysis allowed the most extensive genetic investigation of this taxon. Our findings demonstrate that genes encoding Restriction/Modification (R/M) systems constitute a substantial part of the B. breve variable gene content (or variome). Using the methylome data generated by SMRT sequencing, combined with targeted Illumina bisulfite sequencing (BS-seq) and comparative genome analysis, we were able to detect methylation recognition motifs and assign these to identified B. breve R/M systems, where in several cases such assignments were confirmed by restriction analysis. Furthermore, we show that R/M systems typically impose a very significant barrier to genetic accessibility of B. breve strains, and that cloning of a methyltransferase-encoding gene may overcome such a barrier, thus allowing future functional investigations of members of this species.
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