Characterization of Ornithobacterium hominis colonization dynamics and interaction with the nasopharyngeal microbiome in a South African birth cohort.

Ornithobacterium hominis is a recently described Gram-negative bacterium that colonizes the human nasopharynx and may be associated with poor upper respiratory tract health. Here, we describe the isolation of O. hominis from samples collected from a South African birth cohort, creating the first archive of cultured strains of the species from Africa. Sequenced genomes from this archive reveal that South African O. hominis is more similar to Australian strains than those from Southeast Asia and that it may share genes with other members of the microbiome that are relevant for virulence, colonization and antibiotic resistance. Leveraging existing microbiome data from the cohort, O. hominis was found to be closely associated with bacterial co-colonizers that are rare in non-carrier individuals, including Suttonella, Rappaport, Helcococcus, Lwoffella, Moraxella and Gracilibacteria. Their collective acquisition has a significant impact on the diversity of nasopharyngeal communities that contain O. hominis. Individuals who have not yet acquired O. hominis have a higher abundance of Lwoffella lincolnii than individuals who never acquire O. hominis, suggesting that this could be a precursor state for successful colonization.