University of Leicester
The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.pdf (1.3 MB)

The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

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journal contribution
posted on 2019-10-18, 14:18 authored by M Ventura, F Turroni, A Zomer, E Foroni, V Giubellini, F Bottacini, C Canchaya, MJ Claesson, F He, M Mantzourani, L Mulas, A Ferrarini, B Gao, M Delledonne, B Henrissat, P Coutinho, M Oggioni, RS Gupta, Z Zhang, D Beighton, GF Fitzgerald, PW O'Toole, D van Sinderen
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.


This work was financially supported by the Italian Award for Outstanding Young Researcher scheme Incentivazione alla mobilità di studiosi stranieri e italiani residente all'estero 2005–2009 and a Marie Curie Reintegration Grant (MERG-CT-2005-03080) to MV; by the Science Foundation Ireland Alimentary Pharmabiotic Centre located at University College Cork to DvS, GFF, and PWOT; and by an EMBARK postdoctoral grant to AZ. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.



PLoS Genetics, 2009, 5(12): e1000785.

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The sequence reported in this article has been deposited in the GenBank database (accession number CP001750).