title: The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.
abstract: Bifidobacteria, one of the relatively dominant components of the human intestinal microbiota, are considered one of the key groups of beneficial intestinal bacteria (probiotic bacteria). However, in addition to health-promoting taxa, the genus Bifidobacterium also includes Bifidobacterium dentium, an opportunistic cariogenic pathogen. The genetic basis for the ability of B. dentium to survive in the oral cavity and contribute to caries development is not understood. The genome of B. dentium Bd1, a strain isolated from dental caries, was sequenced to completion to uncover a single circular 2,636,368 base pair chromosome with 2,143 predicted open reading frames. Annotation of the genome sequence revealed multiple ways in which B. dentium has adapted to the oral environment through specialized nutrient acquisition, defences against antimicrobials, and gene products that increase fitness and competitiveness within the oral niche. B. dentium Bd1 was shown to metabolize a wide variety of carbohydrates, consistent with genome-based predictions, while colonization and persistence factors implicated in tissue adhesion, acid tolerance, and the metabolism of human saliva-derived compounds were also identified. Global transcriptome analysis demonstrated that many of the genes encoding these predicted traits are highly expressed under relevant physiological conditions. This is the first report to identify, through various genomic approaches, specific genetic adaptations of a Bifidobacterium taxon, Bifidobacterium dentium Bd1, to a lifestyle as a cariogenic microorganism in the oral cavity. In silico analysis and comparative genomic hybridization experiments clearly reveal a high level of genome conservation among various B. dentium strains. The data indicate that the genome of this opportunistic cariogen has evolved through a very limited number of horizontal gene acquisition events, highlighting the narrow boundaries that separate commensals from opportunistic pathogens.
authors.affiliation: Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology, and Evolution, University of Parma, Parma, Italy. marco.ventura@unipr.it
authors.forename: Marco
authors.initials: M
authors.lastname: Ventura
authors.forename: Francesca
authors.initials: F
authors.lastname: Turroni
authors.forename: Aldert
authors.initials: A
authors.lastname: Zomer
authors.forename: Elena
authors.initials: E
authors.lastname: Foroni
authors.forename: Vanessa
authors.initials: V
authors.lastname: Giubellini
authors.forename: Francesca
authors.initials: F
authors.lastname: Bottacini
authors.forename: Carlos
authors.initials: C
authors.lastname: Canchaya
authors.forename: Marcus J
authors.initials: MJ
authors.lastname: Claesson
authors.forename: Fei
authors.initials: F
authors.lastname: He
authors.forename: Maria
authors.initials: M
authors.lastname: Mantzourani
authors.forename: Laura
authors.initials: L
authors.lastname: Mulas
authors.forename: Alberto
authors.initials: A
authors.lastname: Ferrarini
authors.forename: Beile
authors.initials: B
authors.lastname: Gao
authors.forename: Massimo
authors.initials: M
authors.lastname: Delledonne
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.forename: Pedro
authors.initials: P
authors.lastname: Coutinho
authors.forename: Marco
authors.initials: M
authors.lastname: Oggioni
authors.forename: Radhey S
authors.initials: RS
authors.lastname: Gupta
authors.forename: Ziding
authors.initials: Z
authors.lastname: Zhang
authors.forename: David
authors.initials: D
authors.lastname: Beighton
authors.forename: Gerald F
authors.initials: GF
authors.lastname: Fitzgerald
authors.forename: Paul W
authors.initials: PW
authors.lastname: O'Toole
authors.forename: Douwe
authors.initials: D
authors.lastname: van Sinderen
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D001483:Base Sequence; D001644:Bifidobacterium / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity; D001692:Biological Transport / Q000235:genetics; D010861:Fimbriae, Bacterial / Q000235:genetics; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D020071:Interspersed Repetitive Sequences / Q000235:genetics; D009055:Mouth / Q000382:microbiology*; D020411:Oligonucleotide Array Sequence Analysis; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic; D037521:Virulence Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D037521:Virulence Factors