Bruce J. Paster, PhD

The major research objective of the Paster laboratory is to develop methods for the rapid identification and enumeration of oral microorganisms so that we may elucidate their roles in oral and systemic diseases. We utilize a number of molecular techniques, such as nucleic acid sequencing, gene amplification via polymerase chain reaction, gene cloning, DNA probe development, DNA hybridization, in situ hybridization and, more recently, DNA microarrays.

Identification of Cultivable and Uncultivable Bacterial Species

Using gene amplification via polymerase chain reaction (PCR) and gene cloning, we are able to determine the 16S rRNA sequences from microorganisms that are not presently cultivable. Briefly, 16S rRNA genes from environmental samples are PCR-amplified, using bacterial-universal and selective primers, and are subsequently cloned into E. coli plasmid vectors. Partial sequences (approximately 500 bases) of cloned inserts are used to initially determine the phylogenetic identity of a species or its closest relatives by comparison with known sequences. Clinical samples have been analyzed from patients with a range of oral diseases including: caries, periodontitis, refractory periodontitis, acute necrotizing ulcerative gingivitis (ANUG), necrotizing ulcerative periodontitis in HIV+ subjects and noma (a gangrenous stomatitis that primarily affects malnourished children in developing countries). Of the more than 30,000 clones analyzed in these studies, we have identfied over 200 novel species and some of these appear to be associated with oral health or disease. Based on our microbial data and the findings of other investigators, we estimate that there are about 700 different bacterial species that can inhabit the human oral cavity (see www.homd.org for details).

Determination of Bacterial Population Distribution via DNA Hybridization

To provide a rapid, accurate and inexpensive means for characterizing microbial populations in clinical specimens, we have designed DNA probes based upon 16S rRNA sequences. Utilizing our extensive 16S rRNA database, we have developed over 400 DNA probes to identify organisms at the family, genus, species and sub-species level. We have used a PCR-based, reverse-capture checkerboard hybridization methodology to rapidly detect and quantify oral species of Streptococcus and other genera. This assay works well for identifying pure cultures and for detecting and enumerating specific species, higher taxa and the newly identified "uncultivated" species directly in clinical samples. Many of these probes are currently being used for the rapid identification and enumeration of bacteria in our clinical studies at Forsyth. We are currently transitioning the checkerboard to a glass microarray system, termed the Human Oral Microbe Identification Microarray, or HOMIM (see http://mim.forsyth.org). Presently, we can simultaneously test for 300 key oral species on a single microscope slide.

HOMIM is a high sample-throughput technology which allows the simulataneous detection of over 300 of the predominat bacterial species in the oral cavity, including the "uncultivables." HOMIMs and other molecular methods have been used to indentify the potential role of specific bacterial species or bacterial complexes in oral health and infectious diseases, such as periodontitis and caries. However, HOMIM has utility beyond determining bacterial associations with oral health status. Oral microbial profiles may also serve as potential biomarkers for systemic diseases, such as pancreatic cancer, Crohn's disease and heart disease, e.g., an "unhealthy" profile may be an early indicator of disease, the proverbial "canary in the coal mine" of human disease.

Selected Publications

Colombo APV, Boches SK, Cotton SL, Goodson JM, Kent R, Haffajee AD, Socransky SS, Hasturk H, Van Dyke TE, Dewhirst F, Paster BJ. (2009) Comparisons of subgingival microbial profiles of refractory perio-dontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray. J. Periodontol. 80:1421-1432.

Paster BJ, Dewhirst FE. (2009) Molecular microbial diagnosis. Periodontol. 2000 51:38-44.  

Preza D, Olsen I, Willumsen T, Boches SK, Cotton SL, Grinde B, Paster BJ. (2009) Microarray analysis of the microflora of root caries in elderly. Eur. J. Clin. Microbiol. Infect. Dis. 28:509-517.

Preza D, Olsen I, Willumsen T, Boches SK, Cotton SL, Grinde B, Paster BJ. (2009) Diversity and site-specificity of the oral microflora in the elderly. Eur. J. Clin. Microbiol. Infect. Dis. 28:1033-1040.

Olsen I, Preza D, Aas JA, Paster BJ. (2009) Cultivated and not-yet-cultivated bacteria in oral biofilms. Microb. Ecol. Health Dis. 21:65-71.   Preza D, Olsen I, Aas JA, Willumson T, Grinde B, Paster BJ. (2008) Bacterial profiles of root caries in elderly. J. Clin. Microbiol. 46:2015-2021.
 

Lockhart PB, Brennan MT, Sasser HC, Fox PC, Paster BJ, Bahrani-Mouget FK. (2008) Bactermia associated with toothbrushing and dental extraction. Circulation 117(24):3118-3125.

Bahrani-Mougeot FK, Baster BJ, Coleman S, Ashar J, Knost S, Sautter RL, Lockhart PB. (2008) Identification of oral bacteria in blood cultures by conventional versus molecular methods. Oral Surg. Oral Med. Oral Pathol. Oral Radio.l Endod.105:(6):720-724.

Kawai T, Paster BJ, Komatsuzawa H, Ernst CW, Goncalves RB, Sasaki H, Ouhara K, Stashenko PP, Sugai M, Taubman MA. (2007) Cross-reactive adaptive immune response to oral commensal bacteria results in an induction of receptor activator of nuclear factor-kappaB ligand (RANKL)-dependent periodontal bone resorption in a mouse model. Oral Microbiol. Immunol. 22(3):208-215.

Aas JA, Barbuto SM, Alpagot T, Olsen I, Dewhirst FE, Paster BJ. Subgingival plaque microbiota in HIV positive patients. (2007) J. Clin. Periodontol. 34(3):189-195.

Tanner ACR, Paster BJ, Lu SC, Kanasi E, Kent R, Van Dyke T, Sonis ST. (2006) Subgingival and tongue microbiota of adults with early periodontitis. J. Dent. Res. 85(4) :318-323.

Fox JG, Taylor NS, Howe S, Tidd M, Xu S, Paster BJ, Dewhirst FE. (2006)  Helicobacter anseris sp. nov. and Helicobacter brantaesp. sp. nov., isolated from feces of resident Canada geese in Greater Boston. Appl. Environ. Microbiol. 72(7): 4633-4637.

Paster BJ, Olsen I, Aas JA, Dewhirst FE. (2006) The breadth of bacterial diversity in the human periodontal pocket and other oral sites. Periodontol. 2000 42(1):80-87.

Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. (2005) Defining the normal bacterial flora of the oral cavity. J. Clin. Microbiol. 43(11):5721-5732.

Corby PM, Lyons-Weiler J, Bretz WA, Hart TC, Aas A, Boumenna T, Goss J, Corby AL, Junior HM, Weyant RJ, Paster BJ. (2005) Microbial risk indicators of early childhood caries. J. Clin. Microbiol. 43(11):5753-5759.

Dewhirst FE, Shen Z, Scimeca MS, Stokes LN, Boumenna T, Chen T, Paster BJ, Fox JG. (2005)  Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: Implications for phylogenetic inference and systematics. J. Bacteriol. 187(17):6106-6118.

Wyss C, Dewhirst FE, Paster BJ, Thurnheer T, Luginbühl A. (2005) Guggenheimella bovis gen., sp. nov., isolated from lesions of bovine dermatitis digitalis. Int. J. Syst. Evol. Microbiol. 55(Pt. 2): 667-671.

Shen Z, Xu S, Dewhirst FE, Paster BJ, Pena JA, Modlin IM, Kidd M, Fox JG. (2005)  A novel enterohepatic Helicobacter species 'Helicobacter mastomyrnus' isolated from the liver and intestine of rodents. Helicobacter 10(1):59-70.

Staff

Research Technicians

Sean Cotton
Alexis Kokaras
Christina Murphy

Postdoctoral Fellow
Michael Docktor, M.D.