OralVantage: Comprehensive Database for Disease-associated Oral Bacteria

Objectives: The aim of this study is to generate a database of bacterial genomes associated with oral diseases supported by comprehensive metadata about patients and case presentation.
Methods: Full genome sequences of oral bacterial strains, associated with oral microbiome and diseases, were identified through data mining the Human Oral Microbiome Database, GenBank, and relevant dental literature. Targeted metadata included clinical characteristics and bacterial information. A referential database, OralVantage, of fully annotated genomes with associated metadata was curated using SQLite3 database platform and evaluated for consistency, redundancy, and search ability. A website was built to make OralVantage publically available online. We assessed the frequency of available metadata pertaining patient’s characteristics.
Results: OralVantage contains 412 pathogen full genomes with associated metadata. Patient characteristics include demographics and health status. Bacterial characteristics include date, origin, and site of isolation, genetic/genomic information, and institution information. OralVantage illustrated the ability for searching oral bacteria by disease attributes through cross-referencing clinical presentation with available pathogen genomes. The construction of OralVantage revealed inherent deficiencies in most metadata currently available for oral microbiome genomic research.
Conclusions: OralVantage represents an advantage for dental practice and scientific research investigations, by simplifying data-mining for genomes and associated metadata of suspected oral pathogens. It allows searching common bacterial strains associated with specific clinical conditions, a process usually requiring broad knowledge in oral microbiology and pathogenesis and intensive labor and time con for both daily dental practices and scientists confronted with looking at poorly annotated GenBank files and extensive literature searches. Furthermore, OralVantage provides a model for developing fully annotated oral microbiome repositories.