## 2 Results
### The Composition of the Lung Microbiome and the Levels of SCFAs Are Shaped by the Immune System
Note that the previously reported basal level of inflammation is seen in the lungs of NSG mice [18]. **\(p\) < 0.01, two\(-\)way ANOVA, Tukey post\(-\)test. the expansion of Proteobacteria in the relative absence of strict anaerbe expansion may contribute to the differing susceptibility of Rag1-/- and NSG mice to infection. Figure 5: The lung microbiomes of wild–type, \(Rag1^{-/-}\), and NSG mice display a different composition. Boxplots of the major phyla showing the differences in abundance (expressed as percentage) of NSG and \(Rag1^{-/-}\) mice compared to wild–type mice at each time post infection. Statistical analysis is performed between NSG or \(Rag1^{-/-}\) mice compared to wild–type mice (significance of the zero-mean test on the differences is indicated on top of the corresponding boxplot). ns, not significant,*\(p<0.1\); *\(p<0.05\). Figure 6: Clostridia are expanded in the lung microbiota of \(Rag1^{-/-}\) mice. MW plot of wild–type (**A**), NSG (**B**), and \(Rag1^{-/-}\) (**C**) data at 0 dpi against the other groups. Differential data were calculated using q2–ALDeX2 applied at the class taxonomic level, and significance was evaluated using the [PERSON]’s t–test. Significant classes are shown in red; non–significant classes are shown as grey dots. (**D**) Boxplots of Clostridia showing the differences in abundance (expressed as percentage) of NSG and \(Rag1^{-/-}\) mice compared to wild–type mice at 0 dpi. Consistently, on evaluating the levels of SCFA in the lung of those mice, we found that propanoic, butyric, isobutyric, and valeric acids were increased in the lungs of _Rag1-_-_ mice, while only propanoic acid was slightly increased in NSG mice (Figure 2B). Together, the data show that _Rag1-_, more than NSG, mice had a microbial configuration similar to that of wild-type mice. Further proving that the expansion of Proteobacteria associated with low abundance of strictly anaerobes may correlate with susceptibility to infection, the results in \(p47^{phax-/-}\) mice, a murine model of chronic granulomatous disease (CGD), showed that these mice, while unable to control the fungal growth (Figure 7A,B), in agreement with previous findings [20], showed increased abundance of Proteobacteria (Figure 7C) and reduced levels of Firmicutes (Figure 7C) and SCFAs (Figure 2B). Collectively, these results suggest that, although the distinct genetic immune deficiencies play a major role, the expansion of Proteobacteria may contribute to the susceptibility to infection of NSG mice, while the increase in baseline levels of Bacteroidetes likely promotes protection in _Rag1-_ mice. Therefore, an intact immune system plays a critical role in shaping the composition of the microbiome in response to _Aspergillus_ infection. Figure 7: The increased susceptibility of \(p47^{phax-/-}\) mice associates with a dysbiotic microbiome. Wild\(-\)type and \(p47^{phax-/-}\) mice were infected i.n. with _A. fumigatus_ resting conidia. Mice were assessed for fungal growth (Log10 CFU) in the lungs (**A**), lung histology (periodic acid–Schiff staining, magnification 10\(\times\)) (**B**) and lung microbiome composition (**C**) at 0 and 3 days post-infection. In (**C**), boxplots of the major phyla show the differences in abundance (expressed as percentage) of \(p47^{phax-/-}\) mice compared to wild\(-\)type mice at each time point. Statistical analysis is performed between \(p47^{phax-/-}\) mice compared to wild\(-\)type mice (significance of the zero\(-\)mean test on the differences is indicated on top of the corresponding boxplot). ns, not significant; \({}^{\#}p<0.1;\,^{*}p<0.05\).