This study aimed to define robust respiratory microbiome signatures relevant to the pathophysiology of ARDS and HAP using publicly available data and validation in an independent cohort. Data from 2,177 respiratory samples, including 310 bronchoalveolar lavages (BALs), 1,083 endotracheal aspirates (ETAs) and 784 oropharyngeal swabs (OPSs) obtained from 1,029 critically ill patients was gathered. ARDS and HAP were diagnosed in 223 (21.6%) and 271 (26.3%) patients, respectively. The results of the study showed that the respiratory microbiome dysbiosis associated with HAP and ARDS have specific signatures, which could potentially lead to the development of common and specific innovative microbiome-targeted approaches.