eHOMD has been updated to version 4.1Φ. With this update, a beta version of prophage predictions for all genomes in the eHOMD, is included. We are also transforming the database to a taxonomy based on whole-genome sequence information, while still including 16S rRNA gene-based taxonomy to retain oral taxa known only from their rRNA genes. In this major update, we are adding 44 human oral taxa as well as deleting taxa that whole-genome sequences reveal to be redundant. We present expanded information to indicate which organisms in eHOMD are primarily oral or nasal and which can be found in the mouth but primarily reside at a different body site or in the environment.

eHOMD provides comprehensive curated information on bacteria in the human mouth and aerodigestive tract. Of the 836 taxa in the database, 525 are primarily oral and 22 primarily nasal. Of the oral taxa, 49% are named, 21% unnamed but cultivated and 29% are known only as uncultivated phylotypes. eHOMD taxonomy provides a provisional naming scheme for the currently unnamed taxa, based on both genomic and 16S rRNA sequence phylogeny, so that strain, clone and probe data from any laboratory can be directly linked to a stably named reference scheme.