Molecular Tracking and Cultivation Reveal Ammonia-Oxidizing Archaea as Emerging Commensals of the Human Skin Microbiome

Abstract

BackgroundAmmonia-oxidizing archaea (AOA) have repeatedly been detected on human skin, yet their persistence, physiological traits, and adaptations remain poorly understood. Here, we identify Nitrosocosmicus species as integral members of the healthy skin microbiome using two complementary approaches. ResultsThrough cultivation, we enriched two autotrophic strains, Candidatus Nitrosocosmicus epidermidis and Ca. Nitrosocosmicus unguis, from human skin samples. Genomic analyses revealed specific adaptations for skin colonization, including genomic islands and expanded gene families linked to interactions with host proteins and signaling pathways, distinguishing these AOA from their soil-dwelling relatives. Parallel molecular profiling in cross-sectional and longitudinal cohorts (n=47) consistently detected Nitrosocosmicus particularly in sebaceous areas. Co-occurrence patterns with specific bacterial taxa reinforce their role as stable components of the skin microbiome. ConclusionsThese findings indicate that Nitrosocosmicus species are emerging commensals, evolutionarily capable of transitioning from soil to human skin, where they likely play a critical role in the skin ecosystem.