DNA characterization reveals potential operon-unit packaging of extracellular vesicle cargo from a gut bacterial symbiont

Abstract

Extracellular vesicles (EVs) are lipid bilayer-bound entities secreted by cells across all domains of life, known to contain a range of components, including protein complexes, RNA, and DNA. Recent studies on microbial extracellular vesicles indicate that these virus-sized nanoparticles, 40-90nm in diameter, readily cross the epithelial barrier and reach systemic circulation, can be detected in tissues throughout the body in mice and that 1mL of plasma from healthy humans contains up to one million bacterial EVs. They have been recently recognized for their biologically functional roles, including modulation of bacterial physiology and host-microbe interactions, hence their gain in the microbiome research community’s attention. However, the exact understanding of their functionality is still a subject of active research and debate. Here, we employ long-read DNA sequencing on purified extracellular vesicles from a common mammalian gut symbiont, Parabacteroides goldsteinii, to characterize the genomic component within EV cargos. Our findings challenge the notion of DNA packaging into EVs as a stochastic event. Instead, our data demonstrate that the DNA packaging is non-random. Here, we suggest a novel hypothesis of selective EV-DNA packaging, potentially arranged in operon units, hence providing new insights into our understanding of its genetic makeup and its potential role, underlining the importance of our findings in microbial community dynamics.