Transcriptomic microRNA profiling of dendritic cells in response to gut microbiota secreted vesicles

Extracellular membrane vesicles (MVs) released by gut microbiota are key players in the communication with the host. Next-generation sequencing of small RNAs was used to quantify miRNA expression in monocyte-derived dendritic cells after 24 h-stimulation with MVs isolated from two E. coli intestinal isolates, the probiotic E. coli strain Nissle 1917 (EcN) and the commensal ECOR12. Analysis revealed miRNAs differentially expressed in response to MVs compared to immature control dendritic cells (log2fold-change > 0.7 and padj < 0.001). A common set of miRNAs was modulated by MVs from both strains (46 downregulated, 75 upregulated). In addition, these vesicles elicited differential expression of specific miRNAs depending on the producer strain (26 downregulated and 23 upregulated by EcN; 48 downregulated and 49 upregulated by ECOR12). A total of 9 samples were analyzed, from 3 experimental groups: unstimulated monocyte-derived dendritic cells, stimulated with EcN probiotic vesicles and incubated with vesicles from the commensal strain EcoR12.