Lung and gut microbiota profiling in intensive care unit patients: a prospective pilot study

Gut and lung microbiome play an important role in the host defense and can be predictive of clinical outcome in critically ill patients. However, the interplay between the gut and lung microbiota over time during severe illness is not fully understood and remains to be defined. This study aims to assess the longitudinal changes of the lung and gut microbiota in critically ill patients with and without infection. We performed a prospective, observational cohort study in the intensive care unit (ICU) at Lausanne university hospital. A total of 73 endotracheal aspirates and 93 rectal-swabs were obtained from 38 critically ill adults who required mechanical ventilation. Lung and gut microbiota were characterized using bacterial 16S ribosomal RNA sequencing. The primary outcomes were the bacterial burden, community diversity and community composition of lung and gut microbiota. Secondary outcomes were ICU length of stay and ventilator-free days determined at 28 days after admission. We found a loss of alpha diversity during ICU stay which was more pronounced in infected patients than uninfected patients. The gut microbiome, more than the lung microbiome, became more dissimilar at discharge between uninfected and infected patients.The lung microbiome of patients who developed pneumonia was progressively enriched with Enterobacteriaceae and other Proteobacteria. Alpha diversity index in the lungs and Mogibacterium gut relative abundance predicted the length of mechanical ventilation. Key features of the lung microbiome predicted outcome in critically ill patients. Lung and gut microbiome dysbiosis showed similar trends in critically ill patients and the interplay of gut-lung axis remains yet to be further evaluated.