Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions

Background. It is an important issue whether and how microorganisms can live harmoniously withnormal cells in the circulatory system. Answers to these issues will have enormous impact on medical microbiology. To address these issues, it is essential to identify and characterize the blood-borne microbes in an efficient and comprehensive manner.

Methodology. Traditional approaches using PCR or microarray are not suitable for the purpose due to the complexity and composition of large amount of unknown microbial species in the circulatory system. Recent reports indicated that cell-free DNA (cfDNA) sequencing using advanced sequencing technologies, including next-generation sequencing (NGS) and single-molecule sequencing (SMS) together with associated bioinformatics approaches, possess a strong potential enabling us to address these issues at the molecular level.

Results. Multiple studies using microbial cfDNA sequencing to identify microbes for septic patients have shown strong agreement with cell culture. Similar approaches have also been applied to reveal previously unidentified microorganisms or to demonstrate the feasibility of comprehensive assessment of bloodborne microorganisms for healthy and/or diseased individuals. Single-molecule sequencing (SMS) using either SMRT (single-molecule real-time) sequencing or Nanopore sequencing are providing new momentum to reinforce this line of investigations.

Conclusions. Microbial cfDNA sequencing provides a novel opportunity allowing us to further understand the involvement of blood-borne microbes in development of diseases. Similar approaches should also be applicable to the study of metagenomics for sufficient and comprehensive analysis of microbial species isolated from various environments. This article reviews this line of research and discuss the methodological approaches that have been developed, or are likely to be developed in the future, which may have strong potential to facilitate cfDNA- and cfRNA-based studies of cancer and chronic diseases, in the hope that a better understanding of the hidden microbes in the circulatory system would improve the accuracy of diagnosis, prevention, and treatment of problematic diseases.