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International Team Sequences Genome of Cavity-Causing Bacteria

NEW YORK (GenomeWeb News) – An international group of researchers has sequenced and characterized the genome of a cavity-causing bacterial species called Bifidobacterium dentium, identifying key features that have helped the bug become a tooth decay specialist.

The team, which includes collaborators from Europe, the UK, North America, and Asia, coupled their sequencing and analysis of B. dentium's genome with additional transcriptomic and comparative genomic hybridization studies. The research, which appeared online today in PLoS Genetics, suggests a few key horizontal gene transfer events helped B. dentium shift from a neutral or beneficial commensal microbe to a pathogen involved in tooth decay.

"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," senior author Douwe van Sinderen, a molecular microbiology researcher at the National University of Ireland at Cork, and his colleagues wrote.

Bacteria in the genus Bifidobacterium are commonly found in human and animal gastrointestinal tracts. But while many of these bacteria are considered beneficial, some have been implicated as culprits in dental cavities. One species in particular, B. dentium, seems to be quite common in microbial communities in and around cavities. And researchers suspect that its cavity-causing role is related to its ability to acidify its environment and break down the type of minerals found in teeth.

For the current study, the team used shotgun sequencing to sequence the 2,636,368 base circular genome of a B. dentium strain called Bd1, isolated from a human cavity, to about 10 times coverage.

Their subsequent analysis indicates that the genome contains 55 transfer RNAs and an estimated 2,143 open reading frames. Of these, some 14 percent of ORFs appear to code for proteins participating in carbohydrate transport and metabolism, the researchers noted, consistent with Bifidobacterium's adaptation to the gastrointestinal tract.

Using predicted structure information, the team found evidence suggesting B. dentium contains far more toxin-defence related proteins than another Bifidobacterium species, B. longum subspecies longum.

Overall, the team found 692 B. dentium-specific proteins, many of which also resembled toxin and defence-related proteins.

Together, their findings suggest B. dentium contains genes that help it to not only use nutrients found in mouth and adhere to saliva proteins and plaque bacteria, but also to withstand acidity, antimicrobial compounds, and other assaults it may face in that environment.

Although horizontal gene transfer does not appear to have occurred often in the genome, the team explained, it seems to have played a key role in helping B. dentium snatch up genes that help it thrive as a dental pathogen.

Their subsequent analyses explored everything from B. dentium Bd1's relationship with related microbes to its transcriptome profiles.

For example, based on comparative genomic hybridization involving B. dentium strains from various parts of the body — including those from adult or child cavities, saliva, and fecal samples — and other Bifidobacterium species, the team concluded that there is a great deal of genomic conservation from one B. dentium strain to the next, with B. dentium genomes evolving relatively slowly.

Those involved said the study not only offers new information about B. dentium's parasitic role in the mouth, but also opens the door to more widespread research into the microbiology of tooth decay.

"The genome sequence, when explored using functional genomics approaches, will permit the analysis of genes involved in colonization, survival, growth, and pathobiology of B. dentium in this unique polymicrobial environment," they concluded.

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