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Sequencing Feces and Spit, TIGR Finds Diversity of Organisms in Mouth and Gut

SAVANNAH, Ga., Feb. 8 (GenomeWeb News) - Reporting on a project to sequence the genomes of organisms found in the human gastrointestinal system and oral cavity, a researcher at The Institute for Genomic Research said that a "tremendous diversity" of organisms exists in the two systems.


In December, TIGR announced that it would begin studying the community of microbes found in the oral cavity. More recently, the not-for-profit organization received funding to look at the human gastrointestinal microbiome, according to the researcher, Karen Nelson.


In both studies, TIGR researchers are taking a "metagenomics" strategy to study the organisms' DNA. In other words, the scientists are seeking to sequence all the organisms' DNA en masse, and then identify the various component organisms once they've collected all the sequence data.


Speaking at the annual meeting of the Association of Biomolecular Resource Facilities, held here this week, Nelson said TIGR researchers are analyzing fecal and GI biopsy samples taken from three individuals. Results from their initial analysis show a large variety in the types of organisms present, even with samples taken from the same individual, she said.


The metagenomics study of the human oral cavity involves comparing individuals with healthy mouths with those afflicted with mild to severe periodontal disease, and sequencing the DNA found in seven locations within the mouths of these individuals, Nelson said. Of the estimated 600 different bacteria found in the mouth, only half have been cultured, she added.


According to TIGR, the biofilm scrapings from several sites in the mouth are being collected by a lab headed by Gary Armitage of the Universityof Californiaat San Francisco School of Dentistry. Those samples are sent to David Relman's laboratory at StanfordUniversity, which extracts the DNA and ship the material to TIGR for metagenomic sequencing.


In their preliminary results, Nelson said the TIGR researchers found that 41 percent of the open reading frames they sequenced are novel - that is, no known genes were found to be similar. Several organisms known to inhabit the oral cavity include Porphymonas gingivalis, Prevotella intermedia, and Actinomyces naeslundii.


Nelson added that a tremendous amount of follow-up work is necessary to fully understand the implications of the work, including DNA microarray analysis, comparative genomic hybridization experiments, and studying how these organisms respond to antimicrobials.


But she stressed the efficiency of the metagenomics approach to studying microbial communities, adding that it costs significantly less to sequence the DNA from organisms found in the oral cavity than it does to individually sequence the 12 organisms' genomes.

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