NYU College of Dentistry Shares $1.63 Million NIH Award for Oral Bacteria Identification Study

Although the destructive effects of oral bacteria in producing dental caries (cavities), periodontal disease, and other infectious conditions are well known, the identities of many of the microbes responsible for these conditions, as well as their physical characteristics and ability to grow and sustain themselves, remain a mystery. In fact, only half of the bacteria residing in the human oral cavity have been identified.

Now, a NYU College of Dentistry (NYUCD) microbiologist and an engineer at Sandia National Laboratories, part of the U.S. Department of Energy, are partnering to develop a technology that will facilitate bacterial identification. Their study was recently funded with a three-year, $1.63 million grant from the National Institute of Dental and Craniofacial Research (NIDCR) of the NIH.

The study’s principal investigator, Dr. Anup Singh, Director of Biosynthesis Research at Sandia, uses a method for spotting unknown microbes in saliva dubbed “FISH n’ CHIPs” because it combines fluorescent in situ hybridization (FISH) with a glass chip less than four centimeters wide.

NYUCD, a subcontractor on the grant, received a $264,000 award to acquire saliva samples from NYUCD’s patient population, prepare the samples for Dr. Singh, and analyze Dr. Singh’s findings. Dr. Deepak Saxena, an assistant professor of Basic Science & Craniofacial Biology, is leading the NYUCD study in collaboration with Dr. Daniel Malamud, a Professor of Basic Science & Craniofacial Biology and Director of NYUCD’s HIV/AIDS Research Program.

In their study, Dr. Saxena and Dr. Singh take advantage of recent advances in gene sequencing that enable microbial analysis without lab cultivation. Using probes composed of small, incomplete oral bacteria nucleic acid sequences, the researchers will locate, or “fish out,” bacterial cells with matching DNA sequences from dozens of saliva samples that have been arrayed on a glass chip. Probes that bind to complementary sequences will be marked with a fluorescent dye so that investigators can examine them under a microscope to confirm that they have been properly matched.

The researchers plan to locate cells from a dozen unknown oral bacterial species and establish a bank of cells that can be manipulated in subsequent sequencing studies designed to fully decode a microbe’s genome.

“I anticipate that our ‘FISH n’ CHIPs’ model will ultimately also be used to locate unknown bacteria in the gastrointestinal and nasal tracts and in other part of the body,” said Dr. Saxena. “This will help in the development of genetic tests to identify those at risk for a variety of infectious diseases.”