Welcome to Microbiome
This website offers access to CORE, a streamlined and phylogenetically-curated database of 16S rDNA sequences that represent the core oral microbiome. It was designed to identify bacteria from clinical samples. The website can process large datasets from next generation sequencing runs or single sequence queries. The CORE database is also available for download.
What it contains:
It contains a comprehensive yet minimally redundant set of 16S sequences from the bacteria that regularly reside in the human oral cavity. The classification, based on a phylogenetic maximum likelihood model, offers improved binning accuracy at the level of species, genus and phylum, [ref] and in many cases differs from previous naming.
What it doesn't contain:
The CORE database is not an authoritative resource for accepted nomenclature or reference strains. All sequences are identified by GenBank accession numbers to avoid confusion or ambiguity.
How it was constructed:
Clades of cultivated and uncultivated taxa were formed based on sequence analyses using maximum-likelihood-based topology with bootstrap support, genetic distance, and previous naming. A number of classification inconsistencies for previously named species, especially at the level of genus, were resolved. The database was curated with clinically derived 16S sequences from a large number of subjects and deep sequencing of samples using FLX amplicon pyrosequencing.
How it performs:
The performance of the CORE database for identifying clinical sequences was compared to that of three publicly available databases [ref]. CORE offered improved performance compared to other public databases for identification of human oral bacterial 16S sequences by a number of criteria.
What else is available:
The phylogenetic tree can be viewed or downloaded and provides a framework for measures of community divergence such as UNIFRAC.
How to cite:
Ann L. Griffen1, Clifford J. Beall, Noah D. Firestone, Erin L. Gross, James M. DiFranco, Jori H. Hardman, Bastienne Vriesendorp, Russell A. Faust, Daniel A. Janies and Eugene J. Leys, CORE: A Phylogenetically-Curated 16S rDNA Database of the Core Oral Microbiome, PLoS ONE 6(4): e19051. doi:10.1371/journal.pone.0019051.
The CORE database and website is a joint project of the Griffen-Leys-Beall lab and Dan Janies.
Website constructed by and maintained by Jori Hardman and Noah Firestone.
Supported by NIDCR grants R01DE016125 and R01DE010467, and by an allocation of computing time from the Ohio Supercomputer Center.