Approximately one-third of people carry Staphylococcus aureus in the nose. S. aureus carriage is influenced by a range of factors, including host genetics, lifestyle, and interactions with the nasal microbiota. While previous studies have examined the relationship between S. aureus carriage and the microbiota, most have been underpowered and based on 16S rRNA sequencing, limiting taxonomic and functional resolution.   To address this, we established the CARRIAGE study, comprising 20,000 healthy individuals sampled at three time points, one week apart. From this cohort, we generated shotgun metagenomic data for 7,969 samples at the first time point and 430 participants across all three time points. A stringent decontamination pipeline was applied to remove likely contaminants.   We used unsupervised clustering to define community state types (CSTs) within the nasal microbiota. The most influential taxa driving variation were S. aureus, Dolosigranulum pigrum, Corynebacterium pseudodiphtheriticum, and Corynebacterium accolens. Our results support earlier findings that intermittent carriers have microbiome profiles resembling either persistent carriers or non-carriers. Strain-level analysis revealed that CST is partly shaped by strain-level differences, with longitudinal data confirming the persistence of both CSTs and specific strains over time. Pangenome analyses of dominant strains are ongoing.   These results advance our understanding of the microbial and strain-level factors associated with S. aureus carriage in the human nose.