Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve

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...

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Bibliographic Details
Published in:Nucleic acids research 2018-02, Vol.46 (4), p.1860-1877
Main Authors: Bottacini, Francesca, Morrissey, Ruth, Roberts, Richard John, James, Kieran, van Breen, Justin, Egan, Muireann, Lambert, Jolanda, van Limpt, Kees, Knol, Jan, Motherway, Mary O'Connell, van Sinderen, Douwe
Format: Article
Language:English
Subjects:
Bifidobacterium breve - classification
Bifidobacterium breve - enzymology
Bifidobacterium breve - genetics
DNA Methylation
DNA Modification Methylases - genetics
DNA Restriction Enzymes - genetics
Gene Transfer, Horizontal
Genome, Bacterial
Genomics
Nucleotide Motifs
Phylogeny
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Summary: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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkx1289