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 diseases.

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, Md.

"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, and craniofacial health.