The microbiome is a diverse ecosystem that includes all host-associated microorganisms and their genomes. These microorganisms belong to various kingdoms including some potential pathogens such as bacteria, viruses and fungi. To obtain a comprehensive view of the lung microbiome, including not only bacterial but also viral and fungal data, is of great value to improve our understanding of critical lung illnesses such as VAP or ARDS. The evolution of the lung microbiome over time and the description of its dysbiosis will be key elements to improve diagnosis and preventive measures in ventilated patients.