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Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota

Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored t...

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Autores principales: Heikema, Astrid P., Horst-Kreft, Deborah, Boers, Stefan A., Jansen, Rick, Hiltemann, Saskia D., de Koning, Willem, Kraaij, Robert, de Ridder, Maria A. J., van Houten, Chantal B., Bont, Louis J., Stubbs, Andrew P., Hays, John P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7565314/
https://www.ncbi.nlm.nih.gov/pubmed/32967250
http://dx.doi.org/10.3390/genes11091105
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author Heikema, Astrid P.
Horst-Kreft, Deborah
Boers, Stefan A.
Jansen, Rick
Hiltemann, Saskia D.
de Koning, Willem
Kraaij, Robert
de Ridder, Maria A. J.
van Houten, Chantal B.
Bont, Louis J.
Stubbs, Andrew P.
Hays, John P.
author_facet Heikema, Astrid P.
Horst-Kreft, Deborah
Boers, Stefan A.
Jansen, Rick
Hiltemann, Saskia D.
de Koning, Willem
Kraaij, Robert
de Ridder, Maria A. J.
van Houten, Chantal B.
Bont, Louis J.
Stubbs, Andrew P.
Hays, John P.
author_sort Heikema, Astrid P.
collection PubMed
description Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME (Oxford Nanopore Technologies—ONT, Oxford, UK) and an in-house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 (Oxford Nanopore Technologies—ONT, Oxford, UK) and R9.2 (Oxford Nanopore Technologies—ONT, Oxford, UK) were compared. In conclusion, the current study shows that the nanopore sequencing platform is comparable with the Illumina platform in detection bacterial genera of the nasal microbiota, but the nanopore platform does have problems in detecting bacteria within the genus Corynebacterium. Although advances are being made, thorough validation of the nanopore platform is still recommendable.
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spelling pubmed-75653142020-10-26 Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota Heikema, Astrid P. Horst-Kreft, Deborah Boers, Stefan A. Jansen, Rick Hiltemann, Saskia D. de Koning, Willem Kraaij, Robert de Ridder, Maria A. J. van Houten, Chantal B. Bont, Louis J. Stubbs, Andrew P. Hays, John P. Genes (Basel) Article Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME (Oxford Nanopore Technologies—ONT, Oxford, UK) and an in-house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 (Oxford Nanopore Technologies—ONT, Oxford, UK) and R9.2 (Oxford Nanopore Technologies—ONT, Oxford, UK) were compared. In conclusion, the current study shows that the nanopore sequencing platform is comparable with the Illumina platform in detection bacterial genera of the nasal microbiota, but the nanopore platform does have problems in detecting bacteria within the genus Corynebacterium. Although advances are being made, thorough validation of the nanopore platform is still recommendable. MDPI 2020-09-21 /pmc/articles/PMC7565314/ /pubmed/32967250 http://dx.doi.org/10.3390/genes11091105 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Heikema, Astrid P.
Horst-Kreft, Deborah
Boers, Stefan A.
Jansen, Rick
Hiltemann, Saskia D.
de Koning, Willem
Kraaij, Robert
de Ridder, Maria A. J.
van Houten, Chantal B.
Bont, Louis J.
Stubbs, Andrew P.
Hays, John P.
Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota
title Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota
title_full Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota
title_fullStr Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota
title_full_unstemmed Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota
title_short Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota
title_sort comparison of illumina versus nanopore 16s rrna gene sequencing of the human nasal microbiota
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7565314/
https://www.ncbi.nlm.nih.gov/pubmed/32967250
http://dx.doi.org/10.3390/genes11091105
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