The pulmonary microbiome has emerged as a significant factor in respiratory health and diseases. Despite the sterile conditions maintained during lung perfusion (EVLP), the use of antibiotics in the perfuse liquid can lead to dynamic changes in the lung microbiome. Here, we present the design of a study that aims to investigate the hypothesis that EVLP alters the lung microbiome and induces tissue inflammation. This pilot, prospective, controlled study will be conducted in two Spanish donor centers and will include seven organ donors after brain death or after controlled cardiac death. After standardized retrieval, the left lung will be preserved in cold storage and the right lung will be perfused with EVLP. Samples from bronchoalveolar lavage, perfusion and preservation solutions, and lung biopsies will be collected from both lungs and changes in lung microbiome and inflammatory response will be compared.