Candidatus Ornithobacterium hominis sp. nov.: insights gained from draft genomes obtained from nasopharyngeal swabs

Candidatus Ornithobacterium hominis sp. nov. represents a new member of the Flavobacteriaceae detected in 16S rRNA gene surveys from Southeast Asia, Africa and Australia. It frequently colonises the infant nasopharynx at high proportional abundance, and we demonstrate its presence in 42% of nasopharyngeal swabs from 12 month old children in the Maela refugee camp in Thailand. The species, a Gram negative bacillus, has not yet been cultured but the cells can be identified in mixed samples by fluorescent hybridisation. Here we report seven genomes assembled from metagenomic data, two to improved draft standard. The genomes are approximately 1.9Mb, sharing 62% average amino acid identity with the only other member of the genus, the bird pathogen Ornithobacterium rhinotracheale. The draft genomes encode multiple antibiotic resistance genes, competition factors, Flavobacterium johnsoniae-like gliding motility genes and a homolog of the Pasteurella multocida mitogenic toxin. Intra- and inter-host genome comparison suggests that colonisation with this bacterium is both persistent and strain exclusive.