Respiratory microbiome in mechanically ventilated patients: a narrative review

Abstract

The respiratory microbiome has been less explored than the gut microbiome. Despite the speculated importance of dysbiosis of the microbiome in ventilator-associated pneumonia (VAP) and acute respiratory distress syndrome (ARDS), only few studies have been performed in invasively ventilated ICU patients. And only the results of small cohorts have been published. An overlap exists between bacterial populations observed in the lower respiratory tract and the oropharyngeal tract. The bacterial microbiota is characterized by relatively abundant bacteria difficult to cultivate by standard methods. Under mechanical ventilation, a dysbiosis occurs with a drop overtime in diversity. During VAP development, lung dysbiosis is characterized by a shift towards a dominant bacterial pathogen (mostly Proteobacteria) whereas enrichment of gut-associated bacteria mainly Enterobacteriaceae is the specific feature discriminating ARDS patients. However, the role of this dysbiosis in VAP and ARDS pathogenesis is not yet fully understood. A more in-depth analysis of the interplay between bacteria, virus and fungi and a better understanding of the host-microbiome interaction could provide a more comprehensive view of the role of the microbiome in VAP and ARDS pathogenesis. Priority should be given to validate a consensual and robust methodology for respiratory microbiome research and to conduct longitudinal studies. A deeper understanding of microbial interplay should be a valuable guide for care of ARDS and VAP preventive/therapeutic strategies. We present a review on the current knowledge and expose perspectives and potential clinical applications of respiratory microbiome research in mechanically ventilated patients.

Keywords: 16S rRNA gene; Acute respiratory distress syndrome; Dysbiosis; High-throughput sequencing; Lung microbiome; Mechanical ventilation; Metagenomics; Ventilator-associated pneumonia.

Fig. 1

Bacterial taxonomy, example for Pseudomonas aeruginosa. Adapted from Faner et al. (ref# 6 from the online supplementary material)

Fig. 2

Schematic view of microbiome analysis by high throughput sequencing. Specific stages for bacteria and fungi appeared in blue and those for virus in green

Fig. 3

Alpha and beta diversity for microbiome analysis. On day 0 (D0), endotracheal aspirate of patient A (EA_A0) contained five different OTUs, three of which are common with patient B whose endotracheal aspirate on D0 (EA_B0) contained four different OTUs. Endotracheal aspirate of patient A on D5 (EA_A5) contained only two OTUs: alpha diversity has decreased. In contrast, EA_B5 had five different OTUs on D5: alpha diversity has increased. EA_A and EA_B contained three common OTUs on D0 and only one common OTU on D5, beta diversity has increased

Fig. 4

Influential factors on lung dysbiosis in ventilated patients. Lung microbiome can be altered by a variety of factors, either intrinsic or extrinsic, when intubation and mechanical ventilation are in place. This figure summarizes the main influential factors potentially involved