Background Previous studies reported the significant association between pneumonia outcome and respiratory microbiome. Recently, there has been a rising interest in the roles of bacterial extracellular vesicles (EVs) in several diseases. We studied the composition and function of microbiota- derived EVs in plasma of patients with mechanical ventilation to evaluate whether they have specific features concerning the diagnosis and clinical outcomes. Methods The 114 plasma samples from 57 mechanically ventilated ICU patients (38 pneumonia, 22 nursing-home and hospitalassociated infection [NHAI] group) were prospectively collected on days 1 and 7 in a university hospital. After isolating the bacterial EVs from plasma samples, their nucleic acid was extracted for 16S rRNA gene pyrosequencing and then characterized using α-diversity, β-diversity, intergroup comparison of bacterial composition and predicted functions. Results The PCoA-based clustering of microbial EVs between pneumonia group and non-pneumonia group differed significantly. At the genus level, the proportions of Lactobacillus, Cultibacterium and Sphingomonas were significantly different between pneumonia group and non-pneumonia group. Also, the abundance of Lactobacillus and Bifidobacterium were drastically higher in non-NHAI group than NHAI group. There was a significant difference in the change of β diversity between 28-day survivors and 28-day no-survivors for Bray-Curtis distances (p =0.014). Functional profiling revealed significant difference between pneumonia group and non-pneumonia group. The longitudinal change of EVs gene showed the difference between 28-day survivors and 28-day non-survivors. Conclusions The bacterial microbiota-derived EVs in plasma demonstrated the potential in their use as novel diagnostic biomarkers and prediction markers in patients with mechanical ventilation. Further large prospective studies are needed to test the clinical utility of plasma microbiota-EVs in intubated patients.