Dentistry in the Age of Genomics
Gene-based Discoveries May Help Clinical Wishes Come True: A Conversation with Dr. Bruce Paster

Dr. Bruce J. Paster

Healthy subgingival plaque

Periodontitis subgingival plaque

Bruce J. Paster, PhD, is senior member of the staff and head of the Department of Molecular Genetics and director of the Human Microbe Identification Microarray Core at The Forsyth Institute, and professor of Oral Medicine, Infection and Immunity at the Harvard School of Dental Medicine. 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. The Paster laboratory utilizes 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. In a recent conversation with Global Health Nexus, Dr. Paster addressed the promise and challenges inherent in genomics research.

Global Health Nexus (GHN): How does human genome sequencing impact microbiology?

Dr. Paster: It lets us understand genes that affect the interaction of bacteria with our bodies. Almost more important is the sequencing of the genomes of human-associated bacteria, known as the microbiome. Information from these studies is allowing us to better understand how our microbiome helps us digest our food, how bacteria may cause disease, and, better yet, how bacteria keep us healthy.

GHN: What is Forsyth's role, and your role in particular, in the Human Microbiome Project (HMP) funded by NIH?

Dr. Paster: Forsyth scientists are the major supplier of DNA from oral bacteria to the HMP genome sequencing centers. Forsyth has provided DNA for sequencing of approximately 200 reference genomes. My role has focused on 16S rRNA analysis to better understand the microbial diversity of the oral cavity.

GHN: Many studies focus on a specific group of bacteria associated with oral diseases. How important is it to study genomics in the oral cavity in the effort to improve oral health?

Dr. Paster: It is extremely important to study the genomes of the oral bacteria because we can discover genes involved in disease processes, such as antibiotic resistance genes and toxins. With the availability of the genome sequences of most of the cultivable oral species, data mining will likely reveal much information.

GHN: What are the questions and the challenges involved in doing genomics in the oral cavity?

Dr. Paster: Questions include the following:

  • What bacteria are present in the oral cavity?
  • How stable is the oral microbiome over time?
  • What proteins, enzymes, toxins, etc., does each specific bacterium make?
  • Can genetic factors be identified that control host-bacterial interactions?
  • What is the role of oral bacteria in human health and disease?

Among the challenges are understanding:

  • which of the over 700 common species in the oral cavity are important in health and disease,
  • how the significant variability in the oral microbiome from person to person affects our analyses,
  • how diet and the person's health status may affect the oral microbiome,
  • the complexity of bacterial-host interactions.

GHN: What is the HOMIM project and what is its current status?

Dr. Paster: Since 1986, Dr. Floyd Dewhirst, who is also at the Forsyth Institute, and I have used molecular analyses based on 16S rRNA sequencing to identify over 700 predominant bacterial species in the oral cavity. About 35 percent of these species has not yet been cultivated. Using this information, we developed for our own research the Human Oral Microbe Identification Microarray, known as HOMIM, which allows for the simultaneous detection of about 300 of the most prevalent oral bacterial species, including many that have not yet been cultivated.

Since 2008, HOMIM ( has also been available to the scientific community for the rapid determination of bacterial profiles of clinical samples from the human oral cavity, esophagus, and lung. HOMIM is recognized worldwide as a valuable research tool by many investigators from academic institutions (over 70 teams), government (six teams), and industry (12 companies). Twenty peer-reviewed publications, three reviews describing HOMIM, and many presentations at national and international meetings have resulted from these studies. Under development are microarrays that target bacterial species from the human gastrointestinal tract and the macaque oral cavity.

GHN: What is the relevance of the HOMIM project for oral research?

Dr. Paster: The HOMIM project has tremendous relevance for oral research in the following areas:

  • determining and comparing bacterial associations in oral health and disease, including different types of periodontitis, caries, gingivitis, ventilator-associated pneumonia, endodontic and odontogenic lesions, abscesses, and halitosis,

  • determining the efficacy of therapies; e.g., mouth rinses, antibiotic treatment, scaling and root planing, and laser or periodontal surgery,
  • determining the progression of oral diseases,
  • determining those patients at risk for periodontitis and other oral diseases.

For my own research, I am using HOMIM to identify those microbial species or microbial profiles ("danger profiles") of periodontal sites at risk for developing periodontal disease.

GHN: What have you discovered involving microbial genomics in the oral cavity that have relevance for systemic diseases?

Dr. Paster: HOMIM indeed has utility beyond determining bacterial associations in oral health and oral diseases. Specific oral bacterial species, bacterial complexes, or entire oral microbial profiles, as determined from HOMIM analyses, may serve as potential biomarkers for non-oral systemic diseases. In a recent publication, we noted a significant decrease in overall diversity in the oral microbiome of pediatric Crohn's Disease as compared to that of healthy children and children with ulcerative colitis.

In another study, we reported that there may be oral microbial biomarkers for pancreatic cancer. For example, Neisseria elongata and Streptococcus mitis were detected significantly less often in the saliva of cancer patients than in saliva of healthy controls. In contrast, levels of Granulicatella adiacens were significantly higher in cancer subjects.

GHN: Will these findings lead to changes in the way dentistry is practiced, with specific reference to pathogen-based early detection, which will allow instantaneous chair-side quantification of oral bacteria in plaque or saliva samples?

Dr. Paster: If microbial danger profiles can be used to identify specific sites at risk for periodontal disease, clinicians will be able to focus on those sites for therapy, such as scaling and root planing and localized antibiotic delivery. Progress can be determined after treatment by monitoring the response of the "at risk" microbial profiles; e.g., change to microbial profiles typically detected in healthy sites. Consequently, we may be able to halt disease before it occurs.

For example, with systemic diseases, such as pediatric Crohn's Disease, the presence of certain bacterial species or bacterial complexes in the oral cavity would be indicative of those children who have not yet been diagnosed with the disease. If successful, the impact is huge for Crohn's patients since early diagnosis means prompt and proper treatment, not only for those with Crohn's but for those with other intestinal diseases or disorders. The key here is that this would be a non-invasive diagnostic test—patients would much rather spit in a tube than provide a stool sample, or even be subject to a biopsy.

GHN: Despite global efforts towards prevention and cure of infectious diseases, they remain major problems. What are the implications for using molecular genetic approaches to study various aspects of infectious diseases with respect to prevention and cure?

Dr. Paster: Bacterial identification based on 16S rRNA sequences is much more accurate and rapid at identifying bacterial species than the older phenotypic methods that relied on culture techniques. The molecular methods can also be used to identify microorganisms that cannot presently be cultivated, which represent at least half of all human-associated bacterial species. Who is to say that that those species that you cannot grow are any less important than those you can grow?