CORE: A Phylogenetically-Curated 16S rDNA Database of the Core Oral Microbiome

Abstract

Comparing bacterial 16S rDNA sequences to GenBank and other large public databases via BLAST often provides results of little use for identification and taxonomic assignment of the organisms of interest. The human microbiome, and in particular the oral microbiome, includes many taxa, and accurate identification of sequence data is essential for studies of these communities. For this purpose, a phylogenetically curated 16S rDNA database of the core oral microbiome, CORE, was developed. The goal was to include a comprehensive and minimally redundant representation of the bacteria that regularly reside in the human oral cavity with computationally robust classification at the level of species and genus. Clades of cultivated and uncultivated taxa were formed based on sequence analyses using multiple criteria, including maximum-likelihood-based topology and 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 performance of the CORE database for identifying clinical sequences was compared to that of three publicly available databases, GenBank nr/nt, RDP and HOMD, using a set of sequencing reads that had not been used in creation of the database. CORE offered improved performance compared to other public databases for identification of human oral bacterial 16S sequences by a number of criteria. In addition, the CORE database and phylogenetic tree provide a framework for measures of community divergence, and the focused size of the database offers advantages of efficiency for BLAST searching of large datasets. The CORE database is available as a searchable interface and for download at http://microbiome.osu.edu.

Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing

“…The sequences were modified to reflect the composition of the oral microbiota using full-length 16S rRNA sequences (Griffen et al, 2011). For V1-2, we used a modification of the 27F primer (Lane, 1991), fused to six-nucleotide multiplexing tags and to the 454 FLX sequencing primer A (5 0 -GCCTCCCTCG CGCCATCAGxxxxxxGTTTGATCMTGGCTCAG-3 0 ), where the  region represents the multiplexing tag and the SSU rRNA primer is bold.…”

“…BLAST searches (Altschul et al, 1990) were carried out against our in-house created database of oral 16S rRNA sequences (Griffen et al, 2011). Queries that matched the closest database sequence at X98% identity over an alignment of at least 150 bp were assigned to the respective species-level taxa.…”

“…The remaining unassigned sequences were clustered at 1% divergence using BLAST and a custom PHP script. Clusters with 25 or more members were identified and classified as previously described (Griffen et al, 2011). The data were normalized as percent of total for each taxon for each sample and taxa averaged for the V1 and V4 sequences.…”

“…To construct a reference tree, full-length 16S rRNA sequences obtained from the CORE database (Griffen et al, 2011) aligned according to secondary structure were supplemented with 38 partial sequences obtained during this study that represented novel taxa. The resulting alignment contained 1029 sequences.…”

“…Bacteria may be directly pathogenic or may stimulate damaging host inflammatory responses. The core oral microbiome appears to consist of o1000 species-level taxa (Dewhirst et al, 2010;Griffen et al, 2011), although any number of species may appear transiently in a site so open to the environment.…”