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

Database : the Journal of Biological Databases and Curation
Tsute ChenFloyd E Dewhirst

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 da...Continue Reading

Associated Clinical Trials

Jan 28, 2016·Kim Fasula, Kim Fasula

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Software Mentioned

Excel
MySQL
Yahoo
HMMTigr
HMMPfam
Genome Explorer
MSN
SeqView
BLASTP
Clustal

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