|Title||Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve|
|Author(s)||Bottacini, Francesca; Morrissey, Ruth; Roberts, Richard John; James, Kieran; Breen, Justin Van; Egan, Muireann; Lambert, Jolanda; Limpt, Kees Van; Knol, Jan; Connell Motherway, Mary O.; Sinderen, Douwe Van|
|Source||Nucleic acids research 46 (2018)4. - ISSN 0305-1048 - p. 1860 - 1877.|
|Publication type||Refereed Article in a scientific journal|
Bifidobacterium breve represents one of the most abundant bifidobacterial species in the gastrointestinal 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.