The Leukocyte Landscape Across Mouse Strains and Tissues

ABSTRACT With widespread use of mice ( Mus musculus ) in immunological research, understanding baseline immune variation between mouse models is critical. While peripheral blood immune profiles have been well‐defined, strain‐ and sex‐specific differences in leukocyte composition across other tissues remain poorly characterized. Here, we performed flow cytometric immunophenotyping of 19 leukocyte subsets and 3 T cell memory phenotypes in the blood, bone marrow, liver, spleen, and lymph nodes of seven strains of naïve adult male mice: Balb.b, BALB/c, BALB/c Ly5.1, C57BL/6J, C57BL/6J Ly5.1, BALB/c:B6J (F1), and DBA/2 J. Parallel analyses were conducted in female BALB/c and C57BL/6J mice. Each tissue contained a unique immunobiome, with conventional T and B cells enriched in the lymph nodes and spleen, unconventional T cells and innate lymphoid cells (ILCs) in the liver, and myeloid cells in the bone marrow. Generally, BALB‐derived strains displayed a helper T cell‐ and innate‐skewed profile, enriched for CD4 and regulatory T cells, neutrophils, and natural killer cells. C57BL/6J‐derived strains were typically enriched for CD8 T cells, ILC1s, and conventional dendritic cells, consistent with a cytotoxic immune bias. Small differences were detected between congenic and parental strains. F1's exhibited a mix of C57BL/6J‐biased and intermediate parental phenotypes. DBA/2 J mice were immunologically distinct, notably enriched for γδ T cells. Sex‐associated differences were minor compared to strain effects. These findings provide tissue‐specific benchmarks for leukocyte composition across commonly used mouse strains. They also highlight the importance of strain and sex selection and baseline immunophenotyping to support accurate interpretation of observed immune phenotypes in experimental contexts.