Overview: Bacteria of the genus Haemophilus are abundant in the mouth, making up several percent of the bacteria at most oral sites (Segata et al. 2012, Eren et al. 2014). Members of the genera Haemophilus and Aggregatibacter are closely related and not always cleanly distinguished using short fragments of the 16S ribosomal RNA gene.

Ecological role/importance in health and disease: Of the twelve species recognized in HOMD, one, H. parainfluenzae, is by far the most abundant at most sites within the mouth. Several others, including H. haemolyticus and an unnamed H. sp. HMT 036, are primarily detected on the keratinized gingiva. The opportunistic pathogen H. influenzae is detected with low prevalence in healthy individuals. Other pathogens such as H. aegyptius and H. ducreyi are included in HOMD as reference strains although they are not generally detected in the healthy oral microbiome. The taxon "Terrahaemophilus aromaticivorans", formerly included in HOMD, is now considered a synonym for H. parainfluenzae.