The Human Oral Microbiome Database (eHOMD) is a comprehensive, curated resource providing detailed information on bacteria inhabiting the human mouth and aerodigestive tract. The current version, eHOMD 4.1, incorporates significant updates, including a shift toward whole-genome sequence-based taxonomy, the addition of 44 new oral taxa, deletion of redundant species, and beta predictions for prophages within genomic data. The database stabilizes nomenclature for both named and unnamed species (phylotypes), facilitating the linking of strain, clone, and probe data. Currently, eHOMD catalogs 836 taxa, featuring detailed taxonomic status, cultivation status, genome information (available for 46% of oral taxa), and primary body site assignment, serving as an essential tool for scientific investigation into the oral microbiome.
eHOMD: Comprehensive Information on the Human Aerodigestive Microbiome
Database Overview (HOMD Project Description): The primary goal of HOMD is to provide the scientific community with comprehensive information on approximately 700 prokaryote species found in the human oral cavity. The database links sequence data (genomic and 16S rRNA) with phenotypic, phylogenetic, clinical, and bibliographic information.
eHOMD Version 4.1 Update (V4.1): The major update includes a beta version of prophage predictions for all genomes and a transformation towards a taxonomy based on whole-genome sequence information. It added 44 human oral taxa and deleted redundant taxa.
Taxonomic Composition: Out of 836 total taxa in the database, 525 are primarily oral and 22 are primarily nasal.
Cultivation and Naming Status: For oral taxa, the database classifies them as 49% named, 21% unnamed but cultivated, and 29% known only as uncultivated phylotypes. A provisional naming scheme is provided for unnamed taxa to ensure stability.
Genomic Data Availability: Genome sequences are available for 315 oral taxa (46% of all taxa in HOMD). The platform offers tools like JBrowse Genome Viewer and Genomic BLAST.
Data Organization and Filtering (Taxon Table): The Human Oral/Nasal Microbial Taxa table lists 836 records and allows users to filter based on:
Primary Body Site (Oral, Nasal, Skin, Gut, Vaginal, Pathogen, Environmental, Reference, Unassigned).
Body Site Abundance (High, Medium, Low, Scarce, No Data).
Status (Named/Cultivated, Phylotype, Dropped, etc.).
The table provides specific data points for each Taxon-ID, including Genus, Species, Naming/Cultivation Status, Genome Size range (Mbps), and Genome Count.
Project Support: The HOMD project is funded by Grant RO1-DE016937 from The National Institute of Dental and Craniofacial Research (NIDCR).
Key Takeaway (Publications): The project maintains active publication describing updates and methodologies, including specialized methods for species-level assignment in 16S rRNA datasets and insights into the nostril microbiome.