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Nucleic Acids Res. 2018 Feb 28;46(4):1860-1877. doi: 10.1093/nar/gkx1289.

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

Author information

1
APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland.
2
New England BioLabs, Inc., Ipswich, MA, USA.
3
Nutricia Research, Utrecht, the Netherlands.
4
Laboratory of Microbiology, Wageningen Univerisity, Wageningen.

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.

PMID:
29294107
PMCID:
PMC5829577
DOI:
10.1093/nar/gkx1289
[Indexed for MEDLINE]
Free PMC Article

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