## 3 Discussion  
The results presented in this study follow our previous findings on the role that the delicate balance between strict anaerobes and Proteobacteria in the lung plays in susceptibility to _Aspergillus_ infection [17]. The equilibrium between strict anaerobic bacteria and Proteobacteria is emerging as a common feature in lung disease. Indeed, the healthy lung microbiome is dominated by Bacteroidetes, and a decreased abundance is associated with diseased lower airways [21]. Conversely, the increased abundance of Proteobacteria is a common feature in lung dysfunction and disease, for example in asthma, chronic obstructive pulmonary disease, and cystic fibrosis (CF) [19], and is associated with impaired pulmonary function in patients following hematopoietic stem cell transplantation [22]. Thus, the identification of the mechanisms that keep this equilibrium under control holds great potential for therapeutic purposes. Herein, we show that this balance is influenced by the immune system. Indeed, the lung microbiota of _Rag1-_ mice, deficient in the adaptive immune compartment, and NSG mice, bearing multiple defects in the innate and adaptive immune responses, was characterized by an altered balance between strictly anaerobes and Proteobacteria. Increased abundance of strict anaerobes (Clostridia and Bacteroidetes) and of Proteobacteria was observed in _Rag1-_ and NSG mice, respectively, with the former showing a microbiome configuration associated with resistance and the latter with susceptibility to the infection, as already reported [17]. Despite being heavily expanded in _Rag1-_ at baseline, the relative contribution, if any, of Actinobacteria in infection is presently unknown. Similar to NSG mice, _p47-_ mice expanded pathogenic Proteobacteria in the lung during infection, a finding suggesting that the impaired NADPH oxidase and autophagy and increased inflammasome activity, as observed in CGD mice [20], likely represent important innate pathways contributing to the intimate relationship between host immunity and the microbiome. The influence of the immune system on the composition of the microbiome is not surprising. Indeed, the presence of dysbiosis has been already observed in the gut microbiome in deficiencies of both the innate and adaptive immune compartments [23,24]. However, the possibility of linking specific immune deficiencies to alterations of the lung microbiota associated with a different susceptibility to aspergillus provides opportunities for personalized interventions in high-risk patients by targeting the defective immune component associated with dysbiosis. For instance, it is known that inflammosomes [25] and autophagy [26] regulate the composition of the gut microbiome with relevance in health and disease. Should this apply to the lung, it implicates that anakinra, the recombinant form of the interleukin-1 receptor antagonist, while dampening inflammasome-dependent inflammation in the lung [20,27], likely restores a local protective microbiome. Along this reasoning, autophagy could similarly be targeted to restore the proper microbiome composition. This study also suggests that the direct manipulation of the local microbiome could affect the outcome of aspergillosis. Indeed, we show here that the intranasal instillation of the Proteobacteria _Klebsiella pneumoniae_ increased the susceptibility to infection. This may occur because pneumonia caused by _Klebsiella_ exacerbates the inflammatory response, thus creating the conditions for increased fungal growth. Alternatively, _Klebsiella_ may directly interact with _Aspergillus_, as recently suggested in an in vitro study [28]. Irrespective of the mechanism(s) involved, while bacteria such as _Klebsiella_ may exacerbate fungal pathology, other microbes might play a protective role. This was shown for instance in the protection against pneumococcal colonization upon intranasal administration of _Lactobacillus murinus_[29].