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

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

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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 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

Substances

  • DNA Modification Methylases
  • DNA Restriction Enzymes