Longitudinal microneedle sampling resolves tissue-restricted immune-microbiome dynamics in skin.

The skin microbiome shapes local immunity, but the mechanisms of microbiome-immune crosstalk remain poorly understood. A major barrier to discovery is the lack of approaches that enable simultaneous, longitudinal measurement of microbes and immune cells from the same tissue without disrupting barrier integrity. Here we present a hydrogel-coated microneedle (MN) patch that enables minimally invasive co-sampling of viable microbes, immune cells, and interstitial fluid from skin. In humans, the patches were well tolerated and preserved inter-individual microbial signatures. Murine models colonized with commensal Staphylococcus epidermidis and the opportunistic pathogen Staphylococcus aureus , revealed distinct immune trajectories during commensal colonization, pathogen challenge, and commensal-pathogen co-colonization. Pathogen colonization drives progressive inflammatory amplification, whereas commensal exposure induces controlled immune activation that stabilizes over time. Notably, S. epidermidis reshapes pathogen-induced responses, producing a transient immune activation followed by attenuation of inflammation. These results establish MN sampling as a strategy to resolve immune-microbiome dynamics in barrier tissues and provide a framework for mechanistic studies of host-microbe interactions in health and disease.