NIDCR Launches Unique Initiative on Oral Biofilm
The National Institute of Dental and Craniofacial Research, part
of the National Institutes of Health, has begun supporting an innovative,
three-year study to compile the first full catalogue of genes found
in oral biofilms, the sticky bacteria-laden films that form on our
teeth and gums.
The study, which will yield many tens of thousands of genes exceeding
the number identified in the landmark Human Genome Project will
also attempt to detect unique patterns of gene expression within
these bacterial communities that are predictive of periodontal diseases,
a leading cause of tooth loss that affects millions of Americans.
Once found, these telltale patterns could lead one day to far earlier,
more precise, and more effective diagnosis and treatment of these
The scientists added that all of the biological information will
be stored in a searchable online database that is accessible free
of charge to researchers worldwide. The database also will be home
to an ambitious attempt to sort through the genes with sophisticated
computer software and reassemble the genomes, or complete sets of
genes, for all of the organisms in the oral biofilms. To the extent
this work is successful, large fragments or even full genomes of
microbes that scientists previously could not grow or study in the
laboratory would now be available for research.
"We know that it's going to be tough to sequence the genomes
completely or be certain about the origin of every gene," said
Dr. David Relman, a scientist at Stanford University in Palo Alto,
Ca. and a co-principal investigator on the project with Drs. Stephen
Gill and Karen Nelson of The Institute for Genomic Research in Rockville,
"But just having the raw data will allow everyone to explore
more broadly than ever the physiology of the oral biofilm as a coherent
biological system," he added. "It's at this community
level where we'll take the next big leap forward scientifically
not only in understanding the oral biofilm but in more effectively
preventing a subset of these bacteria from destroying our gums and
decaying our teeth."
Biofilms are sticky, mat-like microbial communities found throughout
nature and many parts of the human body. They typically consist
of hundreds of distinct organisms that cooperate with each other
to adapt to changes in their environment, such as shifts in pH or
the mechanical stress of motion, and ensure their mutual survival.
"With biofilms, the sum is definitely greater than the individual
parts," said Nelson.
To date, researchers have identified over 400 bacteria in the oral
biofilm, but they estimate this number may represent just over half
of the microbes there. Scientists say this shortfall owes to the
fact that many of these microbes cannot be cultivated in the laboratory
or recovered in pure form, making it extremely difficult to understand
how the biofilm functions as an intact community or identify the
subsets of microbes that interact to cause oral infections.
Gill said previous sequencing projects of medically important microbes,
such as the pathogens that cause tuberculosis, gonorrhea, and cholera,
already have provided a wealth of information to researchers. Included
among these new leads are a more detailed understanding of their
physiology, virulence, and potential vulnerabilities.
However, because the oral cavity houses not one but hundreds of
bacteria that interact to cause disease, some have sought new approaches
that comprehensively evaluate the complete biological capabilities
of the various microbes there. This more global view may lead to
novel insights into the interactions among these microbes that maintain
oral health or cause disease, such as periodontitis.
In the newly launched NIDCR-supported study, the scientists will
employ metagenomics, an investigative strategy first proposed nearly
20 years ago but which has become increasingly popular over the
past few years. Metagenomic techniques re-build genomes from small
snippets of DNA collected from a mixture of organisms found in a
distinct place, such as soil or ocean water. In contrast to previous
genomic sequencing studies, the metagenomic approach allows investigators
to obtain the sequence of genes from a complex mixture of organisms,
including those that do not grow in the laboratory directly from
their natural environment.
Once sequenced, the genes can be compared to those already listed
in huge computer databases to determine if they are unique or already
known. Investigators will also determine whether the proteins encoded
by the genes might be produced under varying conditions of health
and disease, providing further insight into the possible role of
the gene in the disease process.
Importantly, researchers will have an opportunity to study the
function and structure of important predicted proteins derived from
these organisms. They will do so by inserting the genes that encode
these proteins into common laboratory bacteria and allowing them
to produce large quantities of the proteins. This means proteins
from previously unknown microbes will now be identified and characterized.
With recent advances in processing and sequencing large amounts
of genetic information, metagenomics has introduced a scale of data
collection rarely, if ever, seen in biology. As published this year,
Venter et al. collected samples of the Sargasso Sea in the central
North Atlantic Ocean and, using a metagenomics approach, sequenced
most of the bacteria present, including many which could not be
grown in the laboratory. The result: over 1.6 billion base pairs,
or units, of DNA and nearly 70,000 new genes.
Gill noted that the oral metagenomics project marks the first time
that this approach has been undertaken for biomedical research on
humans. "The mouth is just so much more readily accessible
than other parts of the body with recognized biofilms, such as the
intestine," he said. "It's a perfect place to start."
Dr. Gary Armitage, a collaborator on this project at the University
of California at San Francisco School of Dentistry, will collect
biofilm scrapings from individuals in either good oral health or
who have various degrees of periodontal disease. The samples will
come from seven sites in the mouth, including the palate, tongue,
cheek, and subgingival crevice. "The idea is to get a global
oral sampling from each person," Nelson said. After extracting
the DNA, the microbial genes represented in the DNA from healthy
individuals will be compared to those found in patients with gingivitis
and various stages of periodontitis. In addition, the investigators
will begin to examine which genes are activated or turned off during
disease. These patterns will be evaluated in larger clinical studies
to validate their use in diagnosing periodontal disease or suggesting
where to most efficiently target treatments.
"This project will provide baseline data for only one disease
state, periodontal disease," said Dr. Lawrence Tabak, NIDCR
director. "But metagenomics can be applied to bacterial populations
present in caries, in people who smoke, or those treated for cancer.
It's a technique that will be extremely beneficial for dental science
and offers another example of the rich biology of the oral cavity."
The National Institute of Dental and Craniofacial Research
is the nation's leading funder of research on oral, dental,