Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics

Abstract Although metagenomics and metatranscriptomics are commonly used to identify bacteria and viruses in human samples, few studies directly compare these strategies. We wished to compare DNA and RNA sequencing of bacterial and viral metagenomes and metatranscriptomes in the human cervix. Total...

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Autores principales: Laila Sara Arroyo Mühr, Joakim Dillner, Agustin Enrique Ure, Karin Sundström, Emilie Hultin
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Publicado: Nature Portfolio 2021
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Acceso en línea:https://doaj.org/article/2a2a6409a3e94dac92e1b50a608cebd7
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spelling oai:doaj.org-article:2a2a6409a3e94dac92e1b50a608cebd72021-12-02T18:48:23ZComparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics10.1038/s41598-021-98452-42045-2322https://doaj.org/article/2a2a6409a3e94dac92e1b50a608cebd72021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-98452-4https://doaj.org/toc/2045-2322Abstract Although metagenomics and metatranscriptomics are commonly used to identify bacteria and viruses in human samples, few studies directly compare these strategies. We wished to compare DNA and RNA sequencing of bacterial and viral metagenomes and metatranscriptomes in the human cervix. Total nucleic acids from six human cervical samples were subjected to DNA and RNA sequencing. The effect of DNase-treatment before reverse transcription to cDNA were also analyzed. Similarities and differences in the metagenomic findings with the three different sequencing approaches were evaluated. A higher proportion of human sequences were detected by DNA sequencing (93%) compared to RNA sequencing without (76%) and with prior DNase-treatment (11%). On the contrary, bacterial sequences increased 17 and 91 times. However, the number of detected bacterial genera were less by RNA sequencing, suggesting that only a few contribute to most of the bacterial transcripts. The viral sequences were less by RNA sequencing, still twice as many virus genera were detected, including some RNA viruses that were missed by DNA sequencing. Metatranscriptomics of total cDNA provided improved detection of mainly transcribed bacteria and viruses in cervical swabs as well as detection of RNA viruses, compared to metagenomics.Laila Sara Arroyo MührJoakim DillnerAgustin Enrique UreKarin SundströmEmilie HultinNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Laila Sara Arroyo Mühr
Joakim Dillner
Agustin Enrique Ure
Karin Sundström
Emilie Hultin
Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics
description Abstract Although metagenomics and metatranscriptomics are commonly used to identify bacteria and viruses in human samples, few studies directly compare these strategies. We wished to compare DNA and RNA sequencing of bacterial and viral metagenomes and metatranscriptomes in the human cervix. Total nucleic acids from six human cervical samples were subjected to DNA and RNA sequencing. The effect of DNase-treatment before reverse transcription to cDNA were also analyzed. Similarities and differences in the metagenomic findings with the three different sequencing approaches were evaluated. A higher proportion of human sequences were detected by DNA sequencing (93%) compared to RNA sequencing without (76%) and with prior DNase-treatment (11%). On the contrary, bacterial sequences increased 17 and 91 times. However, the number of detected bacterial genera were less by RNA sequencing, suggesting that only a few contribute to most of the bacterial transcripts. The viral sequences were less by RNA sequencing, still twice as many virus genera were detected, including some RNA viruses that were missed by DNA sequencing. Metatranscriptomics of total cDNA provided improved detection of mainly transcribed bacteria and viruses in cervical swabs as well as detection of RNA viruses, compared to metagenomics.
format article
author Laila Sara Arroyo Mühr
Joakim Dillner
Agustin Enrique Ure
Karin Sundström
Emilie Hultin
author_facet Laila Sara Arroyo Mühr
Joakim Dillner
Agustin Enrique Ure
Karin Sundström
Emilie Hultin
author_sort Laila Sara Arroyo Mühr
title Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics
title_short Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics
title_full Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics
title_fullStr Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics
title_full_unstemmed Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics
title_sort comparison of dna and rna sequencing of total nucleic acids from human cervix for metagenomics
publisher Nature Portfolio
publishDate 2021
url https://doaj.org/article/2a2a6409a3e94dac92e1b50a608cebd7
work_keys_str_mv AT lailasaraarroyomuhr comparisonofdnaandrnasequencingoftotalnucleicacidsfromhumancervixformetagenomics
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AT karinsundstrom comparisonofdnaandrnasequencingoftotalnucleicacidsfromhumancervixformetagenomics
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