Archaea on human skin: AOA as integral members of the human skin microbiome

[includes the data of enrichments R and T from the Nanopore MinION platform] Ammonia oxidizing archaea (AOA) have been repeatedly detected in the human skin microbiome through molecular and biochemical analyses, yet their persistence, physiology, and adaptations remain poorly understood. Here, we describe two cultivated strains, Candidatus Nitrosocosmicus epidermidis and Nitrosocosmicus unguis, isolated from human skin samples. These strains grow on ammonia and urea as sole energy sources. Genomic islands and expanded gene families in their genomes testify to the capacity of colonizing skin, based on specific interactions with host proteins and signalling cascades and distinct them from their close relatives from soil. Molecular signatures of Nitrosocosmicus ssp. were consistently identified on individuals in cross-sectional and longitudinal cohorts (n=47) with a higher prevalence in sebaceous areas. Co-occurrence network patterns with specific bacteria reinforce the observation that AOA of the genus Nitrosocosmicus form a stable component of the healthy skin and represent emerging commensals in the human microbiome.