Single-Cell RNA Sequencing Reveals Commensal Microbes Amplify Sex-Specific Immune Programming in the Murine Lung: 16S rRNA gene sequencing of pooled fecal samples from SPF mice

ABSTRACT: Sex-based differences in respiratory disease outcomes are well recognized; however, the immunological mechanisms driving this dimorphism remain incompletely understood. While sex hormones influence immune cell development and function, the role of commensal microbes in shaping sex-specific lung immunity has not been fully defined. In a companion lung immune profiling study, we used single-cell RNA sequencing (scRNA-seq) and flow cytometry to compare male and female mice housed under specific pathogen-free (SPF) or germ-free (GF) conditions. Under SPF conditions, males exhibited a striking myeloid bias with increased monocytes and macrophages, broad upregulation of inflammatory mediators (including S100a8, S100a9, and Il1b), and enrichment of TNF and interferon (IFN) signaling pathways. In contrast, females displayed lymphocyte-skewed profiles with higher frequencies of T cells and natural killer (NK) cells. These sex-based differences in immune composition and inflammatory programs were largely absent in GF mice, consistent with microbial exposure amplifying baseline immunological dimorphism between males and females. The present GEO submission provides 16S rRNA gene amplicon sequencing (V3–V4) from cage-level pooled fecal samples collected from SPF male and SPF female cages to verify microbial colonization status in the SPF cohort. Unsurprisingly, DNA from GF samples fell below the threshold for reliable sequencing, consistent with successful maintenance of germ-free conditions. SPF mice harbored relatively diverse bacterial communities, typical of murine gut microbiota. The companion lung scRNA-seq dataset is available in GEO under accession GSE316448.

ORGANISM(S): feces metagenome

PROVIDER: GSE317154 | GEO | 2026/09/01

REPOSITORIES: GEO