The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.

Tsute Chen, Wen Han Yu, Jacques Izard, Oxana V. Baranova, Abirami Lakshmanan, Floyd E. Dewhirst

Research output: Contribution to journalArticle

403 Citations (Scopus)

Abstract

The human oral microbiome is the most studied human microflora, but 53% of the species have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are known primarily from 16S rRNA sequence information. Sequence information tied solely to obscure isolate or clone numbers, and usually lacking accurate phylogenetic placement, is a major impediment to working with human oral microbiome data. The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with a body site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity based on a curated 16S rRNA gene-based provisional naming scheme. Currently, two primary types of information are provided in HOMD--taxonomic and genomic. Named oral species and taxa identified from 16S rRNA gene sequence analysis of oral isolates and cloning studies were placed into defined 16S rRNA phylotypes and each given unique Human Oral Taxon (HOT) number. The HOT interlinks phenotypic, phylogenetic, genomic, clinical and bibliographic information for each taxon. A BLAST search tool is provided to match user 16S rRNA gene sequences to a curated, full length, 16S rRNA gene reference data set. For genomic analysis, HOMD provides comprehensive set of analysis tools and maintains frequently updated annotations for all the human oral microbial genomes that have been sequenced and publicly released. Oral bacterial genome sequences, determined as part of the Human Microbiome Project, are being added to the HOMD as they become available. We provide HOMD as a conceptual model for the presentation of microbiome data for other human body sites. Database URL: http://www.homd.org.

Original languageEnglish (US)
Pages (from-to)baq013
JournalDatabase : the journal of biological databases and curation
Volume2010
DOIs
StatePublished - 2010

Fingerprint

Microbiota
mouth
Databases
microorganisms
genomics
Genes
rRNA Genes
ribosomal RNA
Microbial Genome
Cloning
Bacterial Genomes
microbiome
Human Body
Sequence Analysis
Mouth
Organism Cloning
nucleotide sequences
Clone Cells
genome
phylogeny

ASJC Scopus subject areas

  • Information Systems
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

The Human Oral Microbiome Database : a web accessible resource for investigating oral microbe taxonomic and genomic information. / Chen, Tsute; Yu, Wen Han; Izard, Jacques; Baranova, Oxana V.; Lakshmanan, Abirami; Dewhirst, Floyd E.

In: Database : the journal of biological databases and curation, Vol. 2010, 2010, p. baq013.

Research output: Contribution to journalArticle

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