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

Francesca Bottacini, Ruth Morrissey, Richard John Roberts, Kieran James, Justin Van Breen, Muireann Egan, Jolanda Lambert, Kees Van Limpt, Jan Knol, Mary O. Connell Motherway, Douwe Van Sinderen*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

15 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)1860-1877
Number of pages18
JournalNucleic acids research
Volume46
Issue number4
DOIs
Publication statusPublished - 28 Feb 2018

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