The Human Oral Microbiome: A Status Report

Objectives: For the past six years our group has been supported by NIDCR grant DE016937 to fulfil the following major goals:  1) To create a publically available database with access to a curated taxonomic scheme for provisional naming of the more than 600 oral taxa, and to allow viewing of annotated genomes for all sequenced oral bacteria; 2) To prepare DNA from phylogenetically diverse oral bacteria for genome sequencing by the Human Microbiome Project (HMP) sequencing centers; and 3) To identify isolates of previously uncultivated oral taxa and deposit them with a major culture collection.

Methods: Our approach to this this project has been described extensively in the publication (Dewhirst et al. 2010. J. Bacteriol 192:5002-17).

Results: The HOMD database currently contains 574 annotated genomes of oral bacteria from 184 taxa (multiple genomes being available for a few taxa).  We have sent DNA from 173 oral strains representing 154 taxa to the HMP sequencing centers.  Of the 173 strains, 120 are from named taxa and 53 from unnamed taxa.  Examination of the Wade, Tanner and Moore’s culture collections by 16S rRNA sequencing has allowed us to identify strains for over 200 previously uncultivated oral taxa.  The majority of these isolates represent Human Oral Taxa (HOT) known previously as phylotypes, but a few are totally novel and are assigned new HOT numbers.  These isolates will have their genomes sequenced and be deposited with the BEI/ATCC resource.

Conclusions: Our group has created the Human Oral Microbiome Database as a bioinformatics resource for the scientific community.  We have been the major contributor of highly purified DNA for generating reference genomes for the oral microbiome as part of the HMP.  We have successfully identified strains from a large number of previously uncultivated oral taxa and are making them available through a permanent culture collection.