Collaboration to Build a Better Database

Curators of online databases, in collaboration with laboratories around the world, are assembling the first encyclopedic lists of the thousands of microbes that comprise the human body’s various biofilms, or microbiomes. Both terms refer to the complex polymicrobial communities that form throughout the human body. In the mouth, these communities were primarily known for decades as plaque.
The Human Oral Microbiome Database (HOMD) was launched 2 years ago and is a National Institute of Dental and Craniofacial Research (NIDCR)-supported effort to assemble a range of scientific data on the estimated 1,000 predominant microorganisms that inhabit the oral cavity and adjacent tissues. In a recent analysis of 35,000 oral clone sequences, scientists noted that roughly 35% originated from unnamed and uncultured “phylotypes,” a term roughly akin to “species.” Differences in phylotypes define a species according to the encoded information within its genes, primarily the sequence of the highly conserved 16S ribosomal RNA gene, which scientists have used like a taxonomic fingerprint to group organisms into an evolutionary family tree.
HOMD curators have taken important steps forward: First, they created a taxonomic framework that is anchored on 16S ribosomal RNA gene data. This phylogeny-based framework consists of 619 taxa (species) in 13 phyla (divisions). They hope this more standardized structure will help researchers to communicate better about the inhabitants and diversity of the human oral microbiome. Second, the curators analyzed about 35,000 clone sequences obtained by their laboratories during the past 20 years, in order to validate the initial 619 species in their original taxonomic framework. They also identified 434 additional named and unnamed candidate taxa that, upon further validation, will be added to HOMD. They noted, “…the development of additional bodysite specific curated microbiome resources based on the HOMD model or the framework of the HOMD to be expanded to include the entire human microbiome.” (Source: NIDCR, Science News in Brief, November 23, 2010)