IADR Abstract Archives

The Human Oral Microbiome Database: Updates and New Features

Objective: The Human Oral Microbiome Database (HOMD) is a public database providing comprehensive information on the prokaryotic species present in the human oral cavity. Our team maintains and curates the HOMD with up-to-date information on genomics, phylogeny, and taxonomy for prevalent  human oral microbial species. We have also been developing bioinformatics tools that are integrated into the database for use by the research community. This report summarizes the latest content updates as well as newly available tools and features.

Method: The HOMD was created with PHP, Perl, MySQL and Apache and is hosted on a cluster of computers and housed in the Forsyth Institute Data Center. The HOMD Genomic BLAST was constructed based on the NCBI BLAST+. The new HOMD Genome Browser was implemented based on the “JBrowse” system. Novel human oral taxa were created based on 16S rRNA reference sequences of recently described oral species or recognized phylotypes. New genomic sequences were obtained through the collaboration with the Human Microbiome Project (HMP) sequencing centers and from repositories world-wide.

Result: Currently HOMD contains a total of 688 human oral taxa. Of these, 342 (49.7%) are validly described, 102 (14.8%) unnamed (but cultivated) and 244 (35.5%) known only as uncultivated phylotypes. The current version (13.2) of the 16S rRNA reference sequences contains 831 full length sequences representing prevalent human oral taxa. The HOMD Genomics database currently contains 1292 genomes, representing 325 oral taxa, with either static or dynamic annotations. Additional genomic sequences are being added frequently as they appear at NCBI and other sequence repositories. The HOMD Genomic BLAST and the HOMD JBrowse Genome Browser have also been implemented for searching and navigating among all the human oral microbes with available sequences.

Conclusion: HOMD is a comprehensive bioinformatics resource for the scientific community. HOMD is available at http://www.homd.org.

AADR/CADR Annual Meeting
2014 AADR/CADR Annual Meeting (Charlotte, North Carolina)
Charlotte, North Carolina
2014
979
Microbiology / Immunology
  • Yang, Larry  ( The Forsyth Institute, Cambridge, MA, USA )
  • Chen, Tsute  ( The Forsyth Institute, Cambridge, MA, USA )
  • Izard, Jacques  ( The Forsyth Institute, Cambridge, MA, USA )
  • Tanner, Anne  ( The Forsyth Institute, Cambridge, MA, USA )
  • Wade, William  ( Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, , England )
  • Paster, Bruce  ( The Forsyth Institute, Cambridge, MA, USA )
  • Dewhirst, Floyd  ( The Forsyth Institute, Cambridge, MA, USA )
    • Poster Session
    Oral Microbiology I
    03/21/2014