Niche-specific immune and microbial signatures across the healthy upper respiratory tract mucosa

Host-microbe interactions in the upper respiratory tract (URT) niches that form the first line of defense against respiratory infections are incompletely understood. We profiled immune and microbial features using minimally invasive samples from 44 healthy adults (20–65 years), including nasopharyngeal (NPS), oropharyngeal (OPS), and mid-turbinate nasal swabs (MTSs), mucosal lining fluid (MLF), and saliva. Multiplex cytokine and antibody assays, 16S rRNA sequencing, and pathogen detection by PCR were performed. Immune and microbial profiles differed by niche: nasal samples showed consistently higher antiviral cytokine levels and Corynebacterium dominance. Oral samples had greater microbial diversity with distinct cytokine and antibody patterns. Saliva and MLF had the highest antibody concentrations, predominantly IgA. Integrated analyses identified site-specific microbe-immune associations. These findings show the feasibility of non-invasive, integrated profiling to uncover compartment-specific host-microbe relationships, providing a scalable framework for respiratory mucosal immunology and microbiome research with applications in infection surveillance and vaccine evaluation.