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
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
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 AT joakimdillner comparisonofdnaandrnasequencingoftotalnucleicacidsfromhumancervixformetagenomics AT agustinenriqueure comparisonofdnaandrnasequencingoftotalnucleicacidsfromhumancervixformetagenomics AT karinsundstrom comparisonofdnaandrnasequencingoftotalnucleicacidsfromhumancervixformetagenomics AT emiliehultin comparisonofdnaandrnasequencingoftotalnucleicacidsfromhumancervixformetagenomics
_version_	1718377612622954496

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

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