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the final manuscript.”
“Background Studies of the lung microbiome by culture independent techniques and its impact on lung immunity is a relatively new field and may contribute to new advances in understanding respiratory diseases [1]. Healthy human lungs have up until recently been either considered to be sterile by culture-based techniques, but now new

evidence have identified microbial communities both in healthy humans and in those with disease [2–4]. The human microbiome project [5] did not originally include the lungs, but recently the Lung HIV Microbiome Project has published the first results in this field [6, 7]. Investigations into lung microbiology and lung immunity in humans is limited largely because of technical, ethical considerations and small samples sizes, whereas the use of animal models can provide novel information useful in investigations into the importance of lung microbiome in the development of lung immunology. Effective utilization and development of animal models have recently been identified as one of the most important challenges in future lung microbiome research by the NIH [8]. Whereas many studies have focused on the gut microbiome and its impact on among others lung immunity and asthma, little work has been performed to examine the contribution of the lung microbiome on the pathogenesis of pulmonary diseases. Especially in inflammatory lung diseases such as asthma and COPD, the local microbiome may play an important role in the pathogenesis. The technical challenges related to the novel culture-dependent techniques include consistent extraction of useful DNA, the development of PCR methods and sampling methods for the less abundant bacterial load of the lungs.