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

It is an important issue whether microorganisms can live harmoniously with normal cells in the cardiovascular system. The answer to the question will have enormous impact on medical microbiology. To address the issue, it is essential to identify and characterize the bloodborne microbes in an efficie...

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Autores principales: Chiu, Kuo-Ping, Yu, Alice L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6688590/
https://www.ncbi.nlm.nih.gov/pubmed/31404440
http://dx.doi.org/10.7717/peerj.7426
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author Chiu, Kuo-Ping
Yu, Alice L.
author_facet Chiu, Kuo-Ping
Yu, Alice L.
author_sort Chiu, Kuo-Ping
collection PubMed
description It is an important issue whether microorganisms can live harmoniously with normal cells in the cardiovascular system. The answer to the question will have enormous impact on medical microbiology. To address the issue, it is essential to identify and characterize the bloodborne microbes in an efficient and comprehensive manner. Due to microbial sequence complexity and the composition of significant number of unknown microbial species in the circulatory system, traditional approaches using cell culture, PCR, or microarray are not suitable for the purpose. Recent reports indicate that cell-free DNA (cfDNA) sequencing using next-generation sequencing (NGS) or single-molecule sequencing (SMS), together with bioinformatics approaches, possesses a strong potential enabling us to distinguish microbial species at the nucleotide level. 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. SMS using either SMRT (single-molecule real-time) sequencing or Nanopore sequencing are providing new momentum to reinforce this line of investigation. Taken together, microbial cfDNA sequencing provides a novel opportunity allowing us to further understand the involvement of bloodborne microbes in development of diseases. Similar approaches should also be applicable to the study of metagenomics for sufficient and comprehensive analysis of microbial species living in 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 acute/chronic diseases, in the hope that a better understanding of the hidden microbes in the circulatory system will improve diagnosis, prevention and treatment of problematic diseases.
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spelling pubmed-66885902019-08-11 Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions Chiu, Kuo-Ping Yu, Alice L. PeerJ Bioinformatics It is an important issue whether microorganisms can live harmoniously with normal cells in the cardiovascular system. The answer to the question will have enormous impact on medical microbiology. To address the issue, it is essential to identify and characterize the bloodborne microbes in an efficient and comprehensive manner. Due to microbial sequence complexity and the composition of significant number of unknown microbial species in the circulatory system, traditional approaches using cell culture, PCR, or microarray are not suitable for the purpose. Recent reports indicate that cell-free DNA (cfDNA) sequencing using next-generation sequencing (NGS) or single-molecule sequencing (SMS), together with bioinformatics approaches, possesses a strong potential enabling us to distinguish microbial species at the nucleotide level. 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. SMS using either SMRT (single-molecule real-time) sequencing or Nanopore sequencing are providing new momentum to reinforce this line of investigation. Taken together, microbial cfDNA sequencing provides a novel opportunity allowing us to further understand the involvement of bloodborne microbes in development of diseases. Similar approaches should also be applicable to the study of metagenomics for sufficient and comprehensive analysis of microbial species living in 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 acute/chronic diseases, in the hope that a better understanding of the hidden microbes in the circulatory system will improve diagnosis, prevention and treatment of problematic diseases. PeerJ Inc. 2019-08-06 /pmc/articles/PMC6688590/ /pubmed/31404440 http://dx.doi.org/10.7717/peerj.7426 Text en ©2019 Chiu and Yu https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Chiu, Kuo-Ping
Yu, Alice L.
Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions
title Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions
title_full Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions
title_fullStr Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions
title_full_unstemmed Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions
title_short Application of cell-free DNA sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions
title_sort application of cell-free dna sequencing in characterization of bloodborne microbes and the study of microbe-disease interactions
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6688590/
https://www.ncbi.nlm.nih.gov/pubmed/31404440
http://dx.doi.org/10.7717/peerj.7426
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