title: Identification of restriction-modification systems of Bifidobacterium animalis subsp. lactis CNCM I-2494 by SMRT sequencing and associated methylome analysis.
abstract: Bifidobacterium animalis subsp. lactis CNCM I-2494 is a component of a commercialized fermented dairy product for which beneficial effects on health has been studied by clinical and preclinical trials. To date little is known about the molecular mechanisms that could explain the beneficial effects that bifidobacteria impart to the host. Restriction-modification (R-M) systems have been identified as key obstacles in the genetic accessibility of bifidobacteria, and circumventing these is a prerequisite to attaining a fundamental understanding of bifidobacterial attributes, including the genes that are responsible for health-promoting properties of this clinically and industrially important group of bacteria. The complete genome sequence of B. animalis subsp. lactis CNCM I-2494 is predicted to harbour the genetic determinants for two type II R-M systems, designated BanLI and BanLII. In order to investigate the functionality and specificity of these two putative R-M systems in B. animalis subsp. lactis CNCM I-2494, we employed PacBio SMRT sequencing with associated methylome analysis. In addition, the contribution of the identified R-M systems to the genetic accessibility of this strain was assessed.
authors.affiliation: Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland.
authors.forename: Mary
authors.initials: M
authors.lastname: O' Connell Motherway
authors.affiliation: Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland.
authors.forename: Debbie
authors.initials: D
authors.lastname: Watson
authors.affiliation: Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland.
authors.forename: Francesca
authors.initials: F
authors.lastname: Bottacini
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: Tyson A
authors.initials: TA
authors.lastname: Clark
authors.affiliation: New England Biolabs, Ipswich, Massachusetts, United States of America.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Roberts
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: Jonas
authors.initials: J
authors.lastname: Korlach
authors.affiliation: Danone Nutricia Research, Palaiseau, France.
authors.forename: Peggy
authors.initials: P
authors.lastname: Garault
authors.affiliation: Danone Nutricia Research, Palaiseau, France.
authors.forename: Christian
authors.initials: C
authors.lastname: Chervaux
authors.affiliation: Danone Nutricia Research, Palaiseau, France.
authors.forename: Johan E T
authors.initials: JE
authors.lastname: van Hylckama Vlieg
authors.affiliation: Danone Nutricia Research, Palaiseau, France.
authors.forename: Tamara
authors.initials: T
authors.lastname: Smokvina
authors.affiliation: Alimentary Pharmabiotic Centre and School of Microbiology, National University of Ireland, Cork, Ireland.
authors.forename: Douwe
authors.initials: D
authors.lastname: van Sinderen
mesh_terms: D001483:Base Sequence; D001644:Bifidobacterium / Q000235:genetics*; D019175:DNA Methylation; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods*; D010957:Plasmids / Q000235:genetics; D015183:Restriction Mapping / Q000379:methods*; D017421:Sequence Analysis / Q000379:methods*
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