Increased granulomas in Myd88−/− mice. Myd88−/− mice were administered 109 viable P. acnes intratracheally and were killed after 9 days to test the role of MyD88 in granuloma formation. Naive Myd88−/− mice were used as control mice. (A) Naive (top left) and P. acnes–administered (bottom left) Myd88−/− mouse lungs were removed, fixed, embedded, and examined for granulomas (black arrowheads) via hematoxylin and eosin staining at low magnification (left). Scale bars: 600 μm. At higher magnification in P. acnes–administered mice (right), epithelioid macrophages (red arrowhead) and lymphoid cells (blue arrowhead) can be observed. Scale bar: 200 μm. Granuloma (B) numbers and (C) area were quantified using pattern recognition software SIVQ from three tissue sections 200 μm apart; each individual data point represents the average of those measurements per mouse. (D and E) Naive and P. acnes–administered lungs from Myd88−/− mice were perfused with phosphate-buffered saline, digested into single-cell suspensions, analyzed for cell type composition via flow cytometry, and gated as described in Materials and Methods. The number of total viable (D) lymphoid and (E) myeloid cells is shown. Lymphoid cells are CD4+, CD8+ T cells, and B cells; myeloid cells are AM, TM/MO, DC, and PMN. Statistical significance was determined using unpaired t tests (B), Mann–Whitney tests (C), and multiple t tests (D and E). **P < 0.01, ***P < 0.005, and ****P < 0.0001.