Innovative Metagenomics Strategy Used To Study Oral Microbes

In an innovative new project that could help improve the detection and treatment of oral diseases, scientists are now using a metagenomics strategy to analyze the complex and difficult-to-study community of microbes in the oral cavity.

The project is being led by scientists at The Institute for Genomic Research (TIGR) and Stanford University. It is sponsored by the National Institute of Dental and Craniofacial Research (NIDCR), which is part of the National Institutes of Health.

In recent years, molecular methods have indicated that there are well over 400 species of bacteria in the oral cavity. But, so far, only about 150 of those species have been cultured in laboratories and given scientific names. Using a metagenomics sequencing strategy, TIGR scientists will be able to identify bits and pieces of the DNA of many of those oral microbes that so far have not been grown in labs and studied.

The implications of the project are far-reaching, for some of those bacteria are related to periodontal disease - the chronic infection of the tissues surrounding the teeth that affects nearly 50 million people a year in the United States alone. The study will contrast the oral biofilms in healthy persons and those suffering from periodontitis. Researchers also will examine which genes are activated or turned off when the disease if present.

"The oral project marks the first time that metagenomics has been used on a large scale for biomedical research on humans," says Steven Gill, a TIGR Associate Investigator who is the project's lead investigator. "Because biofilm samples can readily be obtained from the mouth, it's a logical site for initiating a human metagenomics effort."

The mouth's microbial communities tend to congregate in biofilms - sticky, mat-like films that often include hundreds of distinct organisms that cooperate with each other to adapt to changes in their environment. "With biofilms, the sum is definitely greater than the individual parts," says TIGR Associate Investigator Karen E. Nelson, who is a co-investigator on the project.

In the past, TIGR and other labs have concentrated mainly on sequencing the genomes of one bacterium at a time. While that data is extremely useful, scientists believe that a more comprehensive genomic analysis of the hundreds of microbes in the oral cavity will lead to added insights about the bacterial biofilms and the interactions among microbes.

The biofilm scrapings from several sites in the mouth - including the palate, subgingival crevices, tongue, and inner cheek - are being collected by a lab headed by Gary Armitage of the University of California at San Francisco School of Dentistry. Those samples will be sent to David Relman's laboratory at Stanford University, which will extract the DNA and ship the material to TIGR for metagenomic sequencing. That genomic data then will be analyzed by scientists at TIGR and at Relman's lab.

The analysis is expected to find tens of thousands of genes as well as large fragments - in some cases, perhaps full genomes - of oral-cavity bacteria that scientists had not studied previously. Using microarray technology, the scientists will also examine patterns of gene expression in the biofilm communities. Researchers will also study the function and structure of important predicted proteins derived from these organisms. All of the genomic data will be stored in a searchable online database that is accessible free of charge to researchers worldwide.

At TIGR, the oral microbiome sequencing dovetails into an ambitious wider effort to decipher the DNA sequences of an array of bacteria that play roles in periodontal disease. In addition to the oral biofilm analysis, TIGR scientists are at various stages in the sequencing and analysis of the genomes of eight oral-cavity microbes:

* Porphymonas gingivalis, whose genome sequence was published in 2003, plays an important role in periodontal disease. That NIDCR-supported project was led by TIGR's Nelson and Rob Fleischmann in collaboration with scientists at The Forsyth Institute, a research center in Boston, MA.

* Treponema denticola, a spirochete involved in periodontal disease whose closest bacterial relative is the microbe that causes syphilis. That sequence was published in April 2004. TIGR's Ian Paulsen and Rekha Seshadri led the project.

* Prevotella intermedia, a black-pigmented bacterium that has been implicated in many forms of human periodontal diseases, including periodontitis and certain types of gingivitis. John Heidelberg is TIGR's lead researcher on the project.

* Actinomyces naeslundii, a sort of glue bug that is part of the complex of bacteria that are associated with gingivitis. Garry Myers of TIGR is working on it.

* Bacteriodes forsythus, an oral pathogen that has been associated with periodontal diseases, such as chronic and severe adult periodontitis. Gill is leading that team.

* Three Streptococcus species that are early colonizers, growing on the surface of the teeth and forming a substratum of plaque to which secondary colonizing microbes attach, sometimes leading to periodontal disease.

TIGR is compiling a database to compare all sequenced streptococcal species and strains, including three often found in the mouth that are being sequenced: S. gordonii, one of the first colonizers of dental plaque; S. sobrinus, which differs from S. gordonii in that it produces acid which lowers the pH in the oral environment, playing a role in the advent of tooth decay; and S. mitis, yet another early colonizer of tooth surfaces that does not in itself cause disease but may contribute to the later growth of pathogens. Gill and TIGR's Hervé Tettelin are conducting that study.

NIDCR, which is part of the National Institutes of Health, is the nation's leading funder of research on oral, dental and craniofacial health. See the NIDCR press release at: http://www.nih.gov/news/pr/dec2004/nidcr-07.htm