Circulating 16S RNA in Biofluids: Extracellular Vesicles as Mirrors of Human Microbiome?

Abstract

The human body is inhabited by around 10¹³ microbes composing a multicomplex system, termed microbiota, which is strongly involved in the regulation and maintenance of homeostasis. Perturbations in microbiota composition can lead to dysbiosis, which has been associated with several human pathologies. The gold-standard method to explore microbial composition is next-generation sequencing, which involves the analysis of 16S rRNA, an indicator of the presence of specific microorganisms and the principal tool used in bacterial taxonomic classification. Indeed, the development of 16S RNA sequencing allows us to explore microbial composition in several environments and human body districts and fluids, since it has been detected in "germ-free" environments such as blood, plasma, and urine of diseased and healthy subjects. Recently, prokaryotes showed to generate extracellular vesicles, which are known to be responsible for shuttling different intracellular components such as proteins and nucleic acids (including 16S molecules) by protecting their cargo from degradation. These vesicles can be found in several human biofluids and can be exploited as tools for bacterial detection and identification. In this review, we examine the complex link between circulating 16S RNA molecules and bacteria-derived vesicles.

Keywords: 16S; extracellular vesicles; microbiome; plasma.

Figure 1

Structure of the 16S gene. The nine variable regions are depicted in green. Purple bars indicate the portions of the gene mostly used for bacterial classification upon PCR-based amplification and sequencing.

Figure 2

Circulating microbiome analysis. The figure depicts the proposed mechanism of classification of circulating microbiome, based on the isolation of RNA from bacteria-derived extracellular vesicles, amplification of 16S RNA, and Next-Generation Sequencing.