The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.
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.
Ventura
Marco
M
Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology, and Evolution, University of Parma, Parma, Italy. marco.ventura@unipr.it
Turroni
Francesca
F
Zomer
Aldert
A
Foroni
Elena
E
Giubellini
Vanessa
V
Bottacini
Francesca
F
Canchaya
Carlos
C
Claesson
Marcus J
MJ
He
Fei
F
Mantzourani
Maria
M
Mulas
Laura
L
Ferrarini
Alberto
A
Gao
Beile
B
Delledonne
Massimo
M
Henrissat
Bernard
B
Coutinho
Pedro
P
Oggioni
Marco
M
Gupta
Radhey S
RS
Zhang
Ziding
Z
Beighton
David
D
Fitzgerald
Gerald F
GF
O'Toole
Paul W
PW
van Sinderen
Douwe
D
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
D037521:Virulence Factors